Nagito was done phenomenally. Even having accidentally read a spoiler that said he was part of Ultimate Despair he managed to be a really surprising addition to the cast. I think knowing that small detail might have actually thrown me off in guessing the Ultimate Remants reveal earlier than I did as he felt like such a separate entity from the rest of the group.
Chapter 3 had a bunch of red herrings for me. Ibuki absolutely sucking at what was supposed to be her talent felt like it would have a deeper meaning than it did, unless her free time stuff did something extra with that. Other than that I thought her high suggestibility from the disease meant Mikan ordered her to take her own life. Would have been more sinister too and it wouldn't have negatively impacted her plan and lastly I thought the Despair disease would have been one of Junko's more potent tools in spreading global despair.
Well you basically know it's a virtual world by the first minute of the game...after that the self aware jokes were funny but annoying real quick considering how many there are imo.
I don't know. I think the game did it fairly well. They certainly steered you in that way early on, but more so with Usami's comments about the island and her stick than the references, which could easily have been something Monokuma would do in the first. As for the quantity of them, also totally a Monokuma/Junko thing. No self-moderation at all.
I feel like Danganronpa steers you in a certain direction a lot of times, only to flip the script later on or alludes to something only to not bring it up for a very long time so you can't always tell which thing was a red herring or something with a long term payoff. The artificial island hints were brought up early, but were then absent for a very long time, Monokuma jabs aside.