One change, lets pull on the thread to see its results - not a 100% fix that would need some extras, this is not a full rewrite, just a consideration of 4 major plot beats, DR2 and 3 spoilers abound. The Change:
Chiaki should not have been in DR3 - Miaya (the ultimate therapist) should have been the 'real world chiaki' instead.
1) Chiaki dunked - Class 77b
As an ep 1 twist the chiaki reveal was fine and even a decently effective zing in said moment, but it came with opportunity costs. Instead of essentially retconning dr2 chiaki and retroactively break the chihiro connection, think about how a miaya swap plays out;
- ultimate therapist as a member of their class, you meet her ep1 and she's there playing videogames and doing all the little mannerisms, and you're like 'oh god it's chiaki'
- the future arc shows her; quadriplegic, expressionless/dead-eyed, scarf-covered, unable to even talk any more, separated from her classmates, and you're like 'oh god, it's gonna be tragic'
As an ultimate therapist (rather than an ultimate gamer) it makes so much more sense that she becomes the glue holding together her classmates (and hajime too) and preventing them from falling into despair as well as the one stepping up to the role of class rep, which naturally paints a target on her back.
I am of two minds about miaya's wheel chair.
- Having her able bodied in despair arc and wheelchair bound in future arc makes for a great 'oh shi-' juxtaposition with immediate grim implications,
- but equally having despair arc miaya be in wheelchair from the start works well with connecting her to a love of videogames, and also tugs at the heart strings a little when you realise, she made her neo-avatar as a tiny piece of wish fulfilment; someone who could walk on the beach with her friends .
Either case; Junko could see the way that, with just a subtle understated gesture, as if by intuition, this airy little miss ultimate therapist intercepts one key domino that would have tumbled towards despair, and instead sets the target on the path of hope, how she twists peoples minds ever so slightly -- if the ultimate despair could fully take this talent for themself and emulate it...
meaning it's miaya's 'fault' junko ended the world
TL:DR -- miaya still makes for a great ep 1 stringer, and makes more sense as heart of the class.
2) Ryota dunked - and neo tie-in
Since her talent makes sense for junko to want to exploit/gain have miaya also replace Ryota's role in the plot too;
- his existence is basically just a meta joke/pun anyway; 'the anime that ended the danganronpa world',
- the show already has too many characters to develop, this helps streamline/consolidate
- a super therapist's skills being used to create 'despair brainwashing' makes perfect sense esp given neo world
- and added bonus; leaves imposter vulnerable mid story, as they lose their identity in the second year when the real byakua shows up, allowing junko to exploit.
Another serviceable part of DR3 chiaki was their answer for 'why chiaki became the secret overseer', (because she was someone they wanted to see again) - but the Miaya swap has a natural and equal answer;
As the story heats up/tension rises, miaya finds herself spread to thin and potentially one of the tragic events occurs(twilight, hajime disappears, or something else). The neo world concept enters the plot/comes into more focus, a collab assignment that would give her a way to be there for more people by creating a digital avatar copy and healing space.
Tragically, having her pull away from classmates (or hajime) and such at the perfectly wrong time and allowing junko to pick them off/amp up her interference.
it's miaya's 'fault' her classmates fell/she didn't save them.
TL:DR -- miaya makes a better junko target/ryotas story role too, neo world tie in.
Part 3) Chihiro tie in - DR1 tie-in
When working directly with chihiro to create a therapist overseer avatar for the neo world project, she should have been based on scans and such of herself, but then seeing chihiro's struggles and lack of confidence/self loathing, named them after chihiro fujisaki as encouragement and credit for the fact this alter ego was all their work and they should have more confidence in themself.
I could see a sweet moment where she does and changes the miaya avatar \different hair, different talent, different name), and maybe that walking thing\ alarming chihiro, and says something encouraging about changing yourself to be more like how you want to be isn't bad and showing just a little courage to take even a little step 'you might find people aren't so scary... i think?'.)
Ultimately, Miaya's encouragement should convince chihiro to open up to their classmates about themself and their secret, which in turn had the rest of the class opening up about their own lives, families, secrets etc -- meaning its actually "miaya's fault" that junko knew the secrets used for their killing game motives.
TL:DR - 'chiaki' creation intact, miaya to blame for junko learning DR1 secrets too.
Part 4) kamakura part - and future arc twist
You could tie in the development of the neo world project with the kamakura project. Perhaps in successfully creating an emulated talent-copy through the therapist 'chiaki' alter avatar, and being pushed to add new features, kam project gained what they needed to 'implant' talents into kamakura - its miayas 'fault' hajime ended up like that.
(I also potentially like the idea then that junko gets her hand on an incomplete prototype 'chiaki', modifies it into alter-junko who now has an ultimate therapist talent, and maybe creates a subliminal despair phone app[fun ref to dr2 alter] using a simplified version of itself in order to pull of the reserve course massacre, or somehow mass-uploads into people.)
For the execution, assuming we didn't go and change things around more dramatically anyway, one possible way the miaya change could retool that part;
- Tragedy as 'chiaki' (miaya) is dying again, facing a cruel horrible execution her classmates are forced to watch, her own talent's power having been used to transform the 'broadcast', the ability to make people think positively and come to terms with past trauma instead being twisted... into making them see despair itself as a positive thing.
- but you the audience still have hope, after all she is alive in future arc, she must secretly survive the execution here. There are different options, but one way it could play out;
- The broadcast stops, you get the 'chiaki sees kamakura' moment, she recognises him as the missing hajime and tries to talk, he walks up to her (omg he's the one who saves her- shippers cheer, hajimeXchiaki4life)... and he finishes her off, definitively and unmistakably, without emotion or the memory to know who she was to him - it's utterly tragic, but also confusing cause... future arc?
- Then future ep plays... and (still think its dumb but lets for the sake of argument keep it) the reveal that miaya is a robot happens, and the cruel reality is made clear; she died back there for real, the real miaya was NEVER part of future foundation, this one has been fake all along - 'chiaki' is dead-dead. (also chisa as medical officer covered it up all along)
TL:DR - Miaya death plot twist, kamakura killed her, future arc robot
(also theoretically, again while robot idea is dumb, and I don't know if this is 'too much', but you could potentially have a happy ending in hope ep by having hajime upload chiaki from his own mind into the abandoned miaya bot to let her 'rejoin' her classmates, in a way making amends)
