The more I think about it, the more I like the unending series of class trials.
The time loop lasts the duration of a single trial, from the moment the victim dies to the punishment of the Blackened (or the rest of the group, as the case may be). Conveniently, this means that when you're the murderer, you catch yourself red-handed and know you need to stop anyone else from figuring out the truth.
The cast of each loop varies, as does the number of survivors. Sometimes the whole cast is there, except the victim, and everyone is reeling from the unexpected tragedy. Sometimes there's only a few left, jaded veterans of the class trials (except for whoever this timeline's useless comic relief guy is, of course).
On a related note: I imagine the early trials would be the "easy mode". Partly because the non-looping characters are less experienced, partly because the last couple of trials always tie into the greater mysteries (which you won't know in early loops).
Also, Danganronpa plays up the noisy chaos of its class trials. Instead of the orderly witness testimonies of Ace Attorney, or even the rigid structure of a high school debate club, Danganronpa's class trials are big arguments. The "non-stop debates" are framed as cyclical pointless arguments, where people keep saying the same thing over and over until the protagonist fires the right Truth Bullet at the wrong argument.
So to get good at looped class trials, maybe you need to use that chaos as a tool. Or the mechanics might be set up so that the chaos makes things easier. More people making more arguments, which means more opportunities for an innocent to make progress or a Blackened to cause confusion. Or something that fits the other ways later (smaller) trials would tend to be harder.
Oh, and SQ would be the Junko. Both because of their obvious similarities, and because SQ is already tangled in arguably the biggest non-time-loop mystery of the original game. It's either her or Kukrushka, and I don't think Kukrushka has the stage presence.
Though if you were worried SQ as Junko would just be Junko again, you could try to make Kukrushka fill that role. She has backups, after all...
Unfortunately, actually making a fangame that worked like this—dynamically creating murder mysteries like Gnosia dynamically created social deduction scenarios—would probably take a ton of effort. I don't know if the overlap between Gnosia and Danganronpa fandoms can sustain that kind of effort. (TBH, I'm not sure I'd consider myself to be in that overlap. If it wasn't for Demily I wouldn't know the first thing about Danganronpa story structure.)
One fan could theoretically make a fanfic or comic or whatever for this idea, but I'm not sure how well this premise would work without combining the ludic elements of the two series. Without that, it's kinda just a bunch of murder mysteries, without the connective tissue a DR game normally provides or the downtime the Gnosia anime focused on so much.
