Pre-release promotional campaign put a lot of emphasis on the Academy being a prison school, which was a springboard for numerous theories. Were the students all actually hardened criminals? Perhaps after the Tragedy, the world turned its back on Ultimate Talent and had begun imprisoning all promising youngsters to prevent a second Tragedy? In the end, none of it amounted to anything; the school is a closed circle like the previous two, but it supposedly being an actual prison never comes up. The English version calls the school the Ultimate Academy for Gifted Juveniles (as in juvenile hall), which is conspicuous, but it may have been wise to avoid explicitly calling it a prison like in Japanese.
In Love Across the Universe, you can only play through this particular mode as Shuichi. Many fans wanted the option to play through this mode as either Kaede or Shuichi, as the mode would be a far more enjoyable way for Kaede to finish up her Free Time Events with the other students instead of needing to replay the first chapter repeatedly to do so. Not to mention, some fans are curious to see how Kaede would be able to handle the love hotel events if she took over Shuichi's role, and even having the ability to see his own fantasy since he can see hers.
A very interesting rule is established pertaining to double murders in this particular killing game: only the culprit behind the first murder to be discovered is considered a punishable culprit. When the double murder rolls around, Korekiyo is revealed as the culprit behind Tenko's murder relatively early on, but since Angie was the first victim the trial must proceed until the true culprit is discovered. Could be interesting Character Development both for Himiko and Kiyo going forward, no? Imagine having an unambiguously guilty-as-sin culprit survive his trial by sheer luck that someone else acted sooner. But no, turns out that he killed Angie too (which, admittedly, the cast isn't able to prove until he confesses to killing Tenko), so of course, he's executed anyway.
As a result of the aforementioned rule above, a certain brief moment can be this as well. At one point in the trial, Korekiyo states he didn't kill Angie and asks why everyone is looking at him as if he did. This is after the reveal of his "split personality". He said so in a very believable tone that could mislead some players to temporarily believe his other personality killed Angie. While it turned out his Sister form is probably more of a ghost then an actual split personality (like Genocider Syo) and that he did indeed kill both Tenko and Angie, imagine the tragic irony if it was proven Korekiyo and Sister killed one victim each, but only Sister was aware of this. Having found out that his other personality killed the victim whose culprit was meant to be executed after believing he was safe because killing Tenko didn't matter would add for a very nice tragic irony for Kiyo.
In a similar vein, Monokuma clarifies that if there is a tie in the votes for the murder's culprit, the spotless win as long as the blackened is included in the tie. This never actually comes to pass and is used only as a justification for the mastermind to not vote in the final class trial (since she was expecting Keebo to vote for her anyway, automatically rendering her vote null).
The virtual world in Chapter 4. Admit it. You thought it was going to be (and disappointed that it wasn't) Jabberwock Island as a Nostalgia Level. Himiko seems to agree.
Monokuma becomes an active participant in Case 5's trial, but you never have to refute or agree with any of his statements, or get into a Rebuttal Showdown with him. Both could've been interesting concepts, especially needing to agree with him, as it could have provoked interesting reactions from the other students.
Despite being a highlighted and advertised mechanic, the whole "lying" motif hardly gets any mileage in both the gameplay and story progression. The most we get out of it is from Kokichi's trickery and the twists at the end, but the lies you use in the trials aren't used to develop any of the characters (apart from using lies against Kokichi in Chapter 4, which Shuichi isn't even called out on), and they don't leave much impact on the story either. Even in trials where it would be perfect to do so like in Chapters 3 and 4 (the latter of which would have been the perfect opportunity to give Kaito a much more understandable reason to be angry at Shuichi in the following chapter).
The entire plot of the game can be this. The entirety of life on Earth had been completely obliterated centuries ago, with the exception of the sixteen students left in the academy. Even their numbers start to dwindle fast after the start of the killing game, killing each other just to reach the outside world that is not even the empty shell of what it used to be. Upon discovering the shocking truth that they are the last living human beings in existence, the survivors figure that the only thing left they have to live for is to win in the final, ultimate showdown between Hope and Despair... NOPE! None of that matters because it's all actually just a "Truman Show" Plot. Even if you don't hate the real ending of the game, it's easy to miss the "original" plot that basically got discarded.
Shuichi's Free Time Events with Kaede have been subjected to criticism for being a bit too fanservicey in playing up their romance instead of trying to tell more about Kaede's character.
While the idea of a Decoy Protagonist and killing the player character was, admittedly, not a bad one, more than a few fans believe the game could go at it in a much better angle if Shuichi were the decoy and Kaede were the true protagonist. Since he is already so similar to previous protagonists, everyone would believe he is there to stay and when his demise in Chapter 1 happened, it would be much more surprising than Kaede's and having to play the rest of the game as his helper makes it all even more surprising.
In addition to the above, many fans think Shuichi's similarities to the prior protagonists could have been easily overlooked, if not outright justified, if he had been the mastermind instead of Tsumugi. This would have not only made the Decoy Protagonist twist hit even harder as the player would have been unwittingly playing as the Big Bad the entire time who set all this up in the first place, it would have turned the entire game on its head, and have allowed for the severely underutilized lying mechanic to have become a lot more relevant, and useful.
There has been a considerable amount of Korekiyo fans that are disappointed with how his Free Time Events don't tie into his Class Trial at all during Chapter 3. Throughout those events, Korekiyo heavily implies that he was groomed by his sister to enter an incestuous relationship with her and convinced it was okay, and later admits to being captured by a tribe and tortured. Both of these clear up a lot of his behavior when he's revealed as the killer, but this is all pushed aside for a twist that's almost an Ass Pull and everyone else brushing off his behavior as "being weird/creepy".
Since the Ultimate Talent Development Plan boasts every single character having their own story mode and interacting with each other, many people were extremely disappointed that Mukuro is still wearing her "Junko" outfit rather than being herself, preventing her classmates from knowing her as her, even though the first game showed that everyone knew Junko and Mukuro individually. Mukuro herself even laments this at the end of her route.
Also in Ultimate Talent Development Plan, the Future Foundation board members introduced in Danganronpa 3: The End of Hope's Peak High School make an appearance...hidden away on Event squares in the extremely difficult to unlock Future Course, and then only in pixel art form. UTDP would have been a great opportunity to further develop their characters and have them interact more with the video game characters as well as each other. Ryota Mitarai in particular comes to mind since he was in Class 77-B like most of the Danganronpa 2 cast, so we could've expected him to show up once in a while. But there are no Friendly squares on the Future Course that would potentially allow for unique interactions with the Danganronpa 3 cast members, they have no hand-drawn character sprites, voice files, etc. like the video game characters got, nor are they playable in either UTDP itself nor the adjacent bonus mode Despair Dungeon: Monokuma's Test. They would've been really easy to integrate into the latter, since only their pixel sprites would've been required for that bonus mode.
The aforementioned Event squares are also all the same no matter which character you play as. In one of them, you have the option to show a yearbook to Ruruka, Seiko, and Sonosuke, who then get angry at you for reminding them of Hope's Peak Academy and even chase after you when you subsequently flee the scene, which implies that they still got expelled even in the UTDP timeline. You would think this would have been an event specific to Nagito Komaeda, since he was indirectly responsible for their expulsion, but any character can get the exact same thing.
