My natural reaction is to hark on the things I didn't like near the end. So I guess I might as well get those out of the way.
The second half of the last trial was too long winded. Maybe they were trying to get the player to have a better feel of who the Mastermind was since the Mastermind reveal was pretty much at the end. But the speeches went on and on and on about the same thing without adding any substance to the topic at hand which was the conditions outside of the school. I was like if you're going to go on about something, stop wasting my time and give us some specifics.
Amnesia. Usually when you employ amnesia in a storyline, anything could have happened without any clues to both the characters and player. So there's nothing to draw from from a player's standpoint, and the writers can come up with anything during that "unknown" time that you'll have to accept. I just didn't see the point in amnesia in this game. I felt like it was a cheap way of introducing a plot twist. What it really boils down to is that you really don't understand why things have gotten as far as they did because you "forgot." Lame. Yes, there were a few clues, but it was still a weak attempt to introduce a plot twist.
Overall comcept, a great game. I have all the DanganRonpas to date, and I've omly finished the first one. But because I enjoyed the first and what little I know of the other two, I feel like my purchase of all three games will be worth it.