This is an idea that's been kicking around in my head for a while since I used to have a passion for designing fighting game characters. I'm not too savvy on things like frame data, so bear with me here, these are just raw ideas; the concept is more of a pitch than anything else. If you haven't played, seen and read most of the series here, be warned of spoilers.

The Story

  Set in the Future Foundation, the data of powerful Super Highschool Level Students are programmed into the Neo World Program to fight, as a method of training recruits on battling despair. As such, these avatars can kill each other and suffer brutal mutilation to no adverse effects.

Battle System

  As a 2-D fighter, the button map follows a standard light-medium-heavy set up, with all your standard Street Fighter inputs and the like, though given the series' penchant for "Psycho Pop," expect combat to be fairly over-the-top/anime-styled much like Marvel vs. Capcom or any given Arc System Works game (I'm going to avoid mentioning any specific base game till the idea is better realized). The last button would designate some Special Skill exclusive for that character. Since the character's bloodlust is what's building, for our purposes we'll call the usual Hyper Meter the "Despair Meter." Super attacks range from flashy single attacks to transformations which spend 1 bar of your Despair Meter to "Final Killing" attacks that play out like cutscenes and use 3. In most cases, these attacks call back to the character's greater moments in the franchise, or if they're a canon murderer, the way in which they killed their victim.

The Roster

  Sakura Ogami
The Super Highschool Level Fighter, and canonically the strongest human character. The Ryu character, you could say. As you might expect, she carries a few traits of your standard shoto, except maybe a bit more ferocity to keep in line with all the wild battle styles happening here; for one thing, she's one of the few characters to glow with Ki. Some specials attacks include a flying kick, a rekka-series of punches and a Shoryuken. Sakura here has done a lot of interesting stuff throughout the series, so it's a little hard to nail down a good Super besides a certain trial skill Naegi can gain from her called Tranquility, which makes her attacks slightly faster/stronger. Her Special Skill is Breathing Technique, which slowly builds the Despair meter.
  Mondo Owada
The Super Highschool Level Biker Gang Leader. Here's an odd fighter. It's a little hard to compare him to any specific character in another fighting game, but let's just say his command attacks and regular specials are heavily influenced by all the weapons he's been known to carry. He can hit you with his bokken you find in his room during the main game, the Crazy Diamonds pickaxe found on the fifth floor, or he can pull a stop sign out of the ground swing the concrete end around (which was used as an ultimate attack in his appearance in Kenka Banchou Bros: Tokyo Battle Royale). Super attacks include dragging the victim behind him on his motorcycle, calling in the Crazy Diamonds parade to run them down, and his Final Killing is him giving into his rage and breaking all his weapons beating on the victim before smashing their skull in with a dumbbell pulled out of nowhere (he makes great use of the hammerspace). His Special Skill is Upshift and Downshift, which respectively raise his speed at the expense of power, or lower it at the expense of speed: this is signified by him standing tall or slouching casually.
  Genocider Syo / Genocide Jack
The Super Highschool Level Serial Killer. A fairly easy move-set: her playable appearance in Another Episode gives us plenty of material to work from, including Supers; overall she'd operate like the "Vega/Claw" archetype in being highly acrobatic with some long reach to several of her attacks. Her Special Skill would be Trigger Happy, which briefly raises the speed of her attacks. Her Final Killing has her pin the victim to a wall by their limbs before the screen fades into black silhouette against a red background, where the rest of the cutscene plays out to the imagery of Genocider slashing away to her hearts content, before lighting up again to see the crucified victim obscured by shadows, blood leaking down the wall and "Bloodstain Fever/Bloodlust" written beside them.
  Mukuro Ikusaba
The Super Highschool Level Solder. Naturally, this one would be your standard zoner character, fighting with rifles, small arms and her combat knife up close, not unlike Deathstroke in Injustice. She'd also rely on a few special dodging maneuvers to escape, and her Special Skill would add active frames to this dodging special (remember, this girl has never received an injury in her life; she's very good at dodging). Her Final Killing would play out like the ending of DanganRonpa IF: rushing towards the enemy guns blazing, she'd throw a metal spear their way as she drops all her spent weaponry, which they catch between both palms. As the spear is caught, Ikusaba rams the other end with her knee and drives it into their chest before pulling the pin on the grenade she was holding and jumping away from the fiery explosion (that last part was an addition).
  Isshiki Madarai
The Super Highschool Level Bodyguard. Not much to say about this guy, as he lost every fight he appeared in; I think every attack he ever threw was dodged too... well in any case, his secret of being multiple people AKA the Super Highschool Level Multiple Birth Siblings could make for some interesting mechanics, if nothing else: I could picture a Special Skill involving summoning another brother to double up his attacks, or a Final Killing in which all 8 of them gang up on and beat the victim to death. Let's just give this guy a little credit: if he'd been successful, Enoshima would probably be dead and the world saved...
  Hajime Hinata / Izuru Kamukura / Awakening
Reserve Course Student without a talent and "The Super Highschool Level Hope." What am I thinking here, when he confirms in Pekoyama's second free-time event that he can't fight at all? That's sort of the joke really: he's the protagonist-type character who represents the usual investigation-based gameplay, except thrown into a fighting game where his protagonist armor is tested. If you've seen Phoenix Wright fight in UMvC3, you know where I'm going with this: his button map is based around scanning for evidence, picking up said evidence, and his special ability lets him knock enemies off-guard with a Truth Bullet. Depending on how you perform, he can undergo two transformation supers here: he can become the extremely dangerous Izuru Kamukura, who actually can fight, or he can "Awaken" like at the end of the second game and proceed to beat his enemies using his old battle style, but improved upon. In any case, he'd either need to lack a Final Killing or have two separate Final Killings for both forms.
  Akane Owari
The Super Highschool Level Gymnast. As you might imagine, she's highly acrobatic, has excellent walk/run speed and can perform some interesting acrobatic maneuvers, like wall-jumping and head-stomping (ala Chun-Li). Being a non-murderer who loses most of her fights anyway, I can't say much for good attacks and the like for her. In any case, her Special Skill, Peach Muscle, would be good for letting her lengthen the window in which her combos can be strung together, letting her attack for longer. Even if there's not much to go on, you just know she'd be pissed if they made a DR fighting game and she wasn't in it.
  Peko Pekoyama
The Super Highschool Level Swordswoman. As expected, she'd probably operate like a Samurai Showdown character, which should lend her an unfair advantage... except everyone here has some unfair advantage. Her Special Skill, Lightning Flash, would be a counter. She'd also have a Super that briefly lets her replace her bokken with a more damaging actual katana. Her Final Killing is her putting on the KiraKira-chan/Sparkling Justice mask and performing a series of slashes/hits with either the bokken or the katana before winding up with a bat in hand and bashing the victim's skull in. As she does that, the mask falls off and lands beside the body.
  Gundham Tanaka
The Super Highschool Level Breeder. So this depends on how much you believe in this guy's "magic" or not. Either way, he defeated Nidai in canon with just hamsters, so either his control over animals really is that good or he does have access to a few spells; he'd definitely be a zoner with some fairly long start-up on several of his moves. His Special Skill, Infinity Unlimited Flame, could surround him in some small "satellite" animals hovering around him to interrupt certain oncoming attacks. His Final Killing is probably going to remind you of Rolento's "Take No Prisoners" Ultra. Basically, he sends the Four Dark Devas of Destruction to harass the enemy until they step back into the trap he set for them, a magic circle that lights up and surprises them enough for the lasso to easily secure around their feet before he pulls them into the air, hanging upside down. After getting gnawed at by birds, he lets them drop headfirst into the floor, and the magic circle is engulfed in flames.
  Nekomaru Nidai
The Super Highschool Level Coach. As you can imagine, he's the obligatory slow-but-strong character with many powerful grapples. The Power of Life and Death could be his Special Skill, which adds super-armor to his attacks for a short while. According to Mioda, his killing attack is the Super Body Blow he performs on Owari in the second game's second chapter, so I guess we can go with that. Expect a few complex command grapples and some short-but-brutal combos.
  Komaru Naegi
A completely normal girl thrown into dangerous circumstances. Being one of the only characters to actually be playable in an action installment, she has 8 Truth Bullets to draw from for her Megaphone Hacking Gun-based combat (making her a natural zoner character, more so than Ikusaba or Tanaka). She also has a number of interesting skills to choose from, so I'd make her Special Skill Auto-Aim, which as the name suggests, makes her next bullet very likely to hit. Her "Final Killing" would be more like that Break bullet empowered by hope/friendship she fired at the end of Another Episode. Whether it would involve Fukawa... hard to say...
  Takumi Hijirihara
The Killer Killer himself. Not much to be said, but he's frighteningly good with a knife and also excellent at arranging some fairly brutal murder scenes. The guy's fighting style probably needs more research, but I think I can still safely say he could make for an interesting character.
  The Great Gozu
The Former Super Highschool Level Wrestler. I'm hoping we get to see this guy fight more during the course of the new anime season so that he doesn't just get relegated to the "Zangief" character. If nothing else, that elbow drop of his that shattered the floor in episode 2 of the Future Side definitely needs to be a Super.
  Juzo Sakakura
The Former Super Highschool Level Boxer. As the man in charge or riot suppression at the Future Foundation, he gained a reputation as the man that can bring down any despair follower in one punch. So far on the Future Side we've seen him use a lot of weapons and cheap shots, but in Killer Killer he really can kill with a single hit. Like Gozu above, we'll have to see more of him in battle, but if nothing else, he fills the boxer quota for the game.
  Sonosuke Izayoi
The Former Super Highschool Level Blacksmith. Leading weapons development at the Future Foundation, he's the type to carry dozens of knives and kunai under his coat. Again, he's going to need some more interesting fights to fully understand how he'd handle in this game.
  Seiko Kimura
The Former Super Highschool Level Pharmacist. We get a glimpse of what her drugs can do in episode 2 of the Despair Side, and in episode 3 of the Future Side she downs an entire bottle of pills to "hulk out" into some sort of Kyūbi-like form (ala Naruto). At this point she's strong enough to send Izayoi running off with Andou, so clearly she can hold her own against combat-based talents.
  Kyosuke Munakata
The Former Super Highschool Level Student Council President. Presently, we don't quite know how he got so good with a blade, but we see him match swords with Pekoyama in the first episode of the Future Side, so clearly he's not to be taken lightly.
  Kazuo Tengan
The Former Headmaster of Hope's Peak Academy. Based on that last episode of Future Side, he's a great martial artist, able to knock out Sakakura, and his chuusen-firing skills manage to match evenly with Munakata. I could visualize him as a high-execution zoner, with a number of powerful counters for when opponents get in close.
  Monomi / Usami
The "School Trip Advisor/Teacher." Unlike everyone else here, she is playable in a separate mode in Super DanganRonpa 2, in which she defeats minions and Monobeasts by drawing circles around them. We get to see this in better detail in the final cutscene of that same game where she destroys A.I. Junko Enoshima by tying her with a ribbon. Basically, we transfer her top-down perspective gameplay to a 2-D perspective. As for her "Final Killing," it'd be more accurate to say she doesn't have one but simply transforms her in Magical Miracle Girl ★  Usami.

Unlockable Characters

  Kanon Nakajima
Essentially, she'd be a Komaru clone, but with some fairly minor changes. Not much else to say.
  Mechamaru / Mechanidai
Think of Mecha Zangief's relationship on the roster with regular Zangief and you pretty much have this character. He's mechanically similar to Nidai with some slightly changed specials and Supers.
  Kenichirō / Kenshiro
A minor clone of Ogami, like the Akuma to her Ryu.
  Daiya Owada
Again, he'd be the Owada clone with some changed up specials.

The Assists

  Makoto Naegi
"Sore wa chigau yo! / You've got that wrong!": The series staple. I wanted to include it in everyone's move-sets, but it would make zoning characters feel less special. Anything, this one calls out Naegi to stun opponents with a rebuttal. Not much else to be said.
Yasuhiro Hagakure
"A Bad Omen": Hagakure enters the screen and makes a dramatic announcement about something terrible happening to the opponent. To reflect his 30% accuracy, they'll either be abducted by aliens and damaged heavily by it, add seconds to the clock if it's a timed match as a reference to his "Lost In Thought" skill, add to their despair meter as your negative effect, or 10% of the time nothing happens, causing him to face fault and walk away looking dejected. As for the accurate predictions, accurate outcome or not he'll leave announcing "That'll be 1,000,000 yen!"
  Leon Kuwata
"Super Highschool Level Pitch!": Kuwata throws the ball and beans the enemy in the head with perfect precision. This one actually does damage ahead of stunning the target, but also flies high enough to be ducked under.
  Sayaka Maizono
"Your Final Performance": Maizono lunges towards the victim and embeds a kitchen knife in their chest.
  Hifumi Yamada
"For Justice!": Yamada swings the largest Justice Hammer hard enough to spin towards the enemy like a top. Slow-moving, but powerful.
  Celestia Ludenberg
"For My Dream...": Celes approaches the enemy casually before bringing the hammer hidden behind her back crashing down on their skull.
  Yasuke Matsuda
"So noisy...": Looking bored, Matsuda launches a scalpel like a throwing knife before walking away, nose in his favorite manga. This one doesn't damage as heavily as Kuwata's baseball, but can cause victims to bleed out and accumulate damage over time.
  Chiaki Nanami
"Heaven-Slaying Dragon Fist!": It would be a crime not to include this fun little moment from Depsair Side episode 2. Basically Nanami rushes up to the enemy and launches them into the air with a powerful uppercut.
  Nagito Komaeda
"Bad Luck Disaster": This move borders on a Super attack, but it affects the user as well. Based on 3 randomized choices, either a truck will skid across the arena and crash into the players, an airplane might crash into the enemy, or worst of all, a meteor will collide with the field and seriously hurt both players. Having him around is just as much a danger as it is a blessing.
  Kazuichi Souda
"Dream Machine": Souda's favorite project, an actual functioning rocket will launch from the ground in the center of the field. It can catch either player. After the launch, Souda will an impressed-sounding whistle before strolling away.
  Mahiru Koizumi
"Say cheese!": This assist works for longer depending on how close in the victim is. Koizumi blinds the enemy with a camera flash, leaving them briefly off-guard. Being a stickler for good photography, it takes her a while to line up the shot perfectly. After she's done, she'll look at the photo and smile before walking away.
  Teruteru Hanamura
"My Fine Establishment": Hanamura hides under the floorboards (just go with it) and lies in wait as a trap for the enemy. Upon walking over him, he skewers them multiple times just like in the first chapter of SDR2, which can be used to extend combos.
  Ibuki Mioda
"Light Music Passion!": Mioda headbangs wildly and plays her guitar at a heavy distortion combined with her death growls to stun them, before igniting them with a flame thrower built into the neck of her guitar.
  Mikan Tsumiki
"Please Forgive Me!": A scared Tsumiki waits for the enemy to approach and if they enter her zone, she strangles them with rope while pleading forgiveness before injecting them with several syringes.

The Stages

  The Entrance Hall
The place you first meet the other 14 students also stuck in Hope's Peak Academy. The environmental hazard here is the machine guns, which can be used to execute your victim at the end of the match
  The Gymnasium
The place you first meet Monokuma. As expected, the environmental hazard here would be the Spears of Gungnir, which can again be used in an execution finisher.
  The Battlefield Classroom
A bloodstained room Togami finds on the fifth floor of Hope's Peak, which Monokuma claims was left in exactly the state he found it in (though DanganRonpa Zero implies this was the site of Izuru Kamukura's massacre of the Student Counsel). The room is eerily calm and has no hazards at all.
  The Central Island
The place our second crew first meets Monokuma. The Monobeasts ripping characters about with gunfire would be the environmental hazard. Once more, this is able to execute your opponent at the end of the match
  The Beach
Set on the first island of the tropical paradise known as Jabberwock Island. Unlike the other stages, this one lacks a hazard to execute your enemies with, but you can still drop coconuts on the enemy's head if you send them flying into a tree hard enough.
  Outside the Ruins
The password protected setting just outside the second game's final stage on the second island. Just like the entrance hall, the machine guns would be used as the hazard.
  Towa City
The basic setting for Another Episode. The environmental hazards would naturally be the game's Monokuma types, which I go into detail on down below in the Sub-Boss Battles section.
  Arena of The Hero
The setting in which you fight Masaru Daimon. As expected, him and his giant robot "Hero Robot Mark Guyver" will try to kill both players and act as the stage hazard.
  Towa Hills
The setting for the final battle against Monaka in Another Episode. Like Masaru, she'd be the environmental hazard here.

The Sub-Boss Battles

  Monokuma
The Headmaster of Hope's Peak Academy, you knew this annoying little mascot had to be in here, if not playable. Most of his attacks are drawn from his various traps and the manga-influenced attacks he used to beat on Monomi during SDR2.
  Monokuma Army
Inspired by DanganRonpa Another Episode: Ultra Despair Girls and DanganRonpa IF, this stage has you facing off against the weaker mass-produced, A.I. controlled Monokuma, unlike the manually operated version we see normally.
  MonoKing / Big Bang Monokuma
The final boss of Another Episode, this monstrous creature is basically a giant mecha version of the usual thing. See that entire boss battle to know just how many attack patterns this thing has.

The Final Boss

  A.I. Junko Enoshima
Well, she did say she was like a God of War boss in that final trial... (NISA translated it to a Bayonetta reference). Either way, her stage would be the final trial room and she'd have an execution set aside for every single character. This could be abridged in-game, but the full execution could appear in the gallery later. Either way, having a fully animated execution for characters that never got one in canon could make for an interesting draw in this game.

If anyone has any suggestions for characters, assists, stages or even new mechanics, please comment below.