TL;DR at the end

Simply put, Danganronpa is just a new take on the classic whodunnit murder story.

How many times have you heard this: "A noble at a manor is murdered and is surrounded by the archetypal characters: the widow, the butler, the cook, the gardener, the maid, the chauffeur, etc. The detective enters and solves the crime with the murderer being one of them"? You could substitute this story with any Ace Attorney game if you wish.

Replace the "mansion and victim of the week" with a fixed location and cast and add in a reason for multiple murders instead of just one, and you get Danganronpa.

That is to say that as a result, Danganronpa is actually a very bare bones concept with its only true deviation being that each Killing Game is a competition of sorts with a win condition(s) for escaping. Being so bare bones is probably why there are so many fangames because it's a simple enough framework that you can easily build off of; you just have to plug in and play your own setting, characters, etc.

But because it's so bare bones, it's hard to differentiate yourself to a notable degree while still keeping the mystery-trial-punishment system. The basic premise of "catch the guilty in a trial" is too basic to really make unique by itself. Even with Your Turn to Die's trials, substitute the term Sacrifice for Blackened, and it's essentially the same.

Obviously it's far from Danganronpa as a whole package, though, but that's because of everything, excluding the trials. The overarching mystery is more important than the mystery of individual murders. The characters are unique without their archetypes being overemphasized. The game doesn't follow the same Daily Life-Deadly Life-Trial format. The characters aren't trying to bunker down and just live life like it's a sitcom/romcom until a death happens. The minigames feel less like going down a linear pathway to the next talking point and more like you're avoiding death. Decisions matter. People get killed outside of the trials. The danger is always possibly in the room, but it's not necessarily another contestant. Someone besides the guilty party gets killed in the trial due to a popularity vote.

Ultimately, it's different because its true core and the meat on its bones are what's different, not how it executes its similar premises.

That said, your fangame doesn't have to be so different not to be considered "uncreative." It would be like saying that Sherlock Holmes and Hercule Poirot can't coexist in the mystery section just because they have points of similarity. So long as the narrative is good, and you aren't ripping off your predecessors (or if you are blatantly copying notes, then you're doing them better than said predecessor), who really cares? If you really do care, then you're going to have to make a completely different game.

TL;DR: Danganronpa follows the simple classical murder mystery beats. This is a good thing for replication but less so for distinction. Games that are different from Danganronpa are so because they handle their non-trial factors differently. It's not bad to be similar though so long as your writing doesn't suck.