I think Monokuma is a student. Or even one of them, specifically! I think the idea that Monokuma is the 16th student seems to fit well. I have a theory on the identity of this 16th student too. The "murderer" being a member of an extensive cast is the oldest game in the book, but it tends to be always played, even when it seems like it won't happen. The reason for this is just because seeing somebody you know turn out to be BEHIND EVERYTHING is always a surprising and effective twist. The reason most readers never suspect characters, or feel they have no evidence to suspect any characters, always leaves it in the back of the mind but never as a priority in the mystery. Yet time and time again, in ensemble casts like this, it's always a character you know behind it. 999 did this too, even! When it seemed impossible! So why not DR? I mean, it's possibly monokuma is a character we haven't been introduced to yet, but I can't theorize off of that. So.
Without further ado...
Just going off that idea, which could be total bullshit, I feel like it'd be awesome if Monokuma was a student. First off, this theory is going with the idea that an apocalypse happened outside, the cast were all students at the regular academy for a year, and then got their memories wiped somehow (also I think if that's true, for some reason, Kirigiri had her memory SUPER WIPED). It'd make story sense, since the student might have reasons to specifically pick their classmates. But who would it be?
Well Junko sure had a fucking weird, pointless death. Think about it, in a game as tightly put together as this, why just kill off a character as an example that the situation is real. We already saw the Idol, Maizono, die. And when other characters have toyed with Monokuma physically and not been killed, it just seems inconsistent. It's not something a player/reader thinks long about, really, but what about her dying words too? She seemed pretty surprised and said something to the effect of "wait? What?!"
If Junko was in cahoots with Monokuma, that would explain her surprise. She could easily be the mole and the case for her being the mole is stronger than anyone else. But there's something else to her. Naegi had an offhand comment early on about how she looked different in person, instead of in the magazines. Junko makes a joke about Photoshop and the reader probably forgot about it. But what if ... That's because it wasn't Junko?
Think about it. I have no idea why and this is where my theorizing starts revealing itself as baseless, but what if the Junko we saw wasn't Junko at all. The questions are why was she dressed that way and where is the real Junko? My guess is that the only place she could be is that she's fucking Monobear.
That's my only idea on who the 16th Student is. Basically this is all total bullshit where I just try connecting one theory to another baselessly so that it circularly makes sense to itself. But hey, I think it's interesting. Obviously the questions this raises are, or rather, points that shoot it down, are:
* Why would Junko hide herself if everyone had their memories wiped and why would somebody be dressed as her (maybe explained with Junko needing somebody to be Junko so the entire student body was there??? For... some reason that might be important???)
* The mole seemed to be somebody still alive, so if she wasn't the mole, what was her purpose? She clearly has more to her character than being killed as a pointless example and we either learn through more information in the future, or her role isn't done.
* If Junko was monokuma what are her motivations, we know Monokuma is doing it for DESPAIR and being sadistic, so maybe Junko has some bad past???
I dunno, this is total crazy bullshit. It's flimsy, but it's something to think about.