Also, I watched my girlfriend stream Danganronpa, and I'll just say, the writing's always been kinda crap; the game's strong points are definitely not the quality of the writing.
Granted, DR3 really fucked with the lore a lot in ways that 2 and AE did not, but I think that DR3's biggest flaw was partly just the product of the DR veneer wearing off. The more you explain something, the more it inevitably kinda is blah.
My biggest takeaway from DR3, flaws-wise, has been:
1. By including all of the original cast that survived, you create an expectation that they all survive and that some die. The thing is, the writer chose both, seemingly wanting to keep both sides on this issue happy. What he fails to realize is that both sides feel cheated by these damned fakeouts.
2. Ultimately, there was no theming or meaning to any of the NGs. I mean there were, individually, but it just felt incomplete, and at times, it felt like it was bad writing. Koichi opened his hand to save Kyoko? That felt set up, but that's literally impossible to have set up because there are a lot of dominoes to set up for it to happen. The most blatant one is Kyoko dying if Makoto lives to the fourth day, echoing him saving her in the first game. And why did Tengan have such an inconvenient NG? Was he so stupid that he would set himself up with an NG like that?
3. Speaking of Tengan, why the hell did he want to save Makoto? What motivation would he have had to do so? At first I had the inkling that he was verifying Munakata's theory, but now it turns out that his reasons were... nothing. Makoto dying would have benefited his plan explicitly!
4. And speaking of his plan, why was Ryota there? It's implied that he wasn't supposed to be, but the show does not explain why he showed up. They literally could have just said "Chisa invited Ryota" and that'd be it.
5. Why was Miaya such a nothing character? I get why in the literal sense - she died - but it was such a wasted opportunity. Making her be one of the masterminds would have been neat, and ultimately, it would have made sense if she was one given that she had all of the NGs. Plus, how the FUCK did a recording hack her? That's a literal plothole, nothing in the show explains it (unless I'm mistaken and that part wasn't a recording).
6. Munakata either should have left with Class 77 (since he too had fallen prey to despair) or atoned through suicide. Him walking the Earth is... blah.
7. That Nagito was not involved in ANY way in the ultimate final plot of Danganronpa besides being a supporting character makes me feel cheated as a Danganronpa fan. There was SO much setup! Danganronpa 2 showed a person who, before he was ever Ultimate Despair, was twisted, demented, scheming, and sort of evil. It made us intrigued to see what more he could do. We eventually saw this in Another Episode - bad game, but good Nagito (and good Toko). In reality, he was the main villain of AE. Monaca may be the main villain essentially, and Alter Ego Junko may be pulling strings on both ends, but Nagito is playing some fucking 11D chess. We then leave off with him plotting to create the next Junko. In Despair, we get to see more of Nagito's shenanigans in the fourth episode, and even more in future episodes. He's the most important member of 77 besides Chiaki, and thus we are waiting desperately to see what crazy scheme he has up his sleeves. And as Hope rolls along, we find out that it ain't shit. He's JUST reformed. You couldn't even have him come in to thwart his plans, to show that he's grown out of his insanity for hope after having been enlightened by Hajiru being above it all. Shit, not even a line showing that he had finally seen a clashing of two hopes.
8. They go so crazy with the fanservice in the final episode, and they couldn't even give us a scene where Kazuichi finishes Mecha Chiaki!