So just to note, we're still not seeing:
1. Great Gozu
2. Daisaku Bandai
3. Miaya Gekkogahara
In the Despair arc and all three have passed away. Aside from Chisa, every other character appeared in Despair before their death was shown on-screen. I think that there is going to be some relevance to that. With that, I ultimately think that it suggests that the Great Gozu's role in Despair is significant in some respect or another.
I do think that we will see Gekkogahara and Bandai - if only just to give us a little more of them to enjoy (including seeing what the real Gekkogahara is like) - but I think that we haven't seen the Great Gozu because he is the key to all of this. And you know what else? Think about this:
Munakata believes that the goal of the mastermind (he calls the person the attacker, but if we operate on the idea of multiple attackers his terminology is biased based on his preconceptions) is to protect Naegi and get him out safely. In all, here are the people who actively are trying to protect him or have tried:
1. Aoi Asahina
2. Kyoko Kirigiri
3. Great Gozu
4. Miaya Gekkogahara (Monaca Towa)
5. Kazuo Tengan
Of these five, we're going to assume that returning members are not the mastermind, especially Kyoko who shows very little in the way of actively trying to protect Naegi (though not through lack of trying). When you look at the rest of the cast, you have two types: one that doesn't want Makoto dead/has expressed a desire to kill and one that does. Munakata, Juzo, Izayoi, and Ruruka have all expressed a desire to kill Makoto (in the case of Izayoi and Ruruka, both show relatively passive desires). Seiko, Yasuhiro, Kizakura, Bandai, Chisa, and Mitarai have not.
Of the people left - Great Gozu, Monaca Towa, and Kazuo Tengan, the latter two have very strongly defined reasons to keep Makoto alive. Monaca Towa because she is bored and Kazuo Tengan because he does not believe that the killing will eliminate despair. Gozu? Look at what he says and how he says it. He talks about the future of the Future Foundation, he talks about how they "need that power for the future", he talks about how much he moved people with his words/actions. Ultimately, his goals and the speculation of Munakata's line up perfectly - Great Gozu wants the Future Foundation to have the power of Makoto's hope, and the attacker wants the Future Foundation to have the power of Makoto's hope. Of course, this assumes that Munakata is correct in his speculation, but I do think that he is not just a rambling lunatic. I am going to go one step forward and say that the Great Gozu killed Chisa in order to spur Munakata to action and create the situation that would require Munakata to be killed and for the mutual killing game to end as a result. Going back further, there's also the fact that his eyes glow red, which from what I recall, has only ever happened with the Remnants of Despair (we don't even see this happen with Ultimate Despair!).
However, I do not believe that the Great Gozu is the big bad. I do believe that he is dead, hence Kyoko covering his face. Which begs the question, who could be it? For me, the list is:
1. Chisa Yukizome - It would be strange to have the two villains (three if we operate on the idea that Mitarai is involved) both be dead, but it would be a very interesting twist - creating a situation where Munakata has no need to kill anyone at this stage and will therefore kill for no reason. Chisa also knows more than anyone what her death would do to him.
2. Koichi Kizakura - A bit more obvious, especially since someone pointed out that he keeps his left hand in his pocket at all times only after he wakes up, and if we assume that his NG is taking his hand out of his pocket, he would have to be very lucky and fortunate to just happen to have his hand in his pocket. I also sort of subscribe to the theory that Kizakura is Ultimate Despair and the father of Junko and Mukuro.
3. Ryota Mitarai - Also obvious, but to such an extent that it feels like it won't happen. I do kind of expect that he is involved - at the very least, he understands why everything is happening (perhaps not by who, and why he will not say I don't know) - but Despair is raising the face-heel turn flag so quickly that it doesn't feel like it will be him. Danganronpa has never really been that blunt before about these kinds of big twists. With Izuru, the earliest we got was the flashback - while I've seen some people deduce that it could be Hajime, most of the people don't get it - and they don't notice that both of them say "...this world", which for Hajime is what triggered the memory. With Junko, it was a little earlier that they hinted at it - disregarding the hint at the beginning of the game - but it was an easy hint to miss in episode 5.
4. Nagito Komaeda - And here we have the fourth obvious choice. Nagito has expressed a desire, repeatedly, to be there to witness the moment when two great hopes collide. What kind of disappointment would it be when that actually finally happened? Because we never once did see him get his wish. What good is his talent if he was so unlucky that he would not be able to bear witness to this?
For me, I think that these four are the only candidates, and seem to be the only ones that people seriously discuss for mastermind status. Tengan would be out there, the returning cast are more for "wouldn't it be surprising if..." fodder, Ando gives too few shits about hope and despair, Munakata is too affected by anything to have been double-agenting, Juzo is dumb, and the rest are dead (while also not having compelling evidence).
And one final note, we do not have any hints about the following NG codes:
1. Great Gozu
2. Miaya Gekkogahara (as an aside, it stands to reason that the mastermind knows that Miaya is a robot since they put the bracelet on her)
3. Chisa Yukizome (actually, does she even have one?)
4. Ryota Mitarai (though we can speculate that his NG is important in some way)
3 has good reason and 2 is not relevant since we can safely guess that Monaca was probably being truthful; which leads me to wonder if we will ever see Gozu's, and whether his NG is significant. I think it's very possible that we could clean something from his NG, but it's just as possible that it won't ever come up.