Yeah, the monsters are actually the biggest problem... superhumans are the response to the monster threat after all, unless we get some reliable soldiers to fight against the monster faction it doesn't matter wheter Ella or HERO wins their little feud the monsters will still come for humanity and destroy/consume everything. The future after that will be bleak anyway because the tech to make superhumans already exists and is now public knowledge, also Ella was already changing people underground for quite a while so believing that it's possible to erradicate the superhumans when a serum or a pill is all that takes to make a new one at this point is an exercise in futility.
I think the best scenario we can hope for is that whoever wins in the end at least provide some shelter/protection for the people that didn't want to go superhuman, something in line with that number 1 possibility alkeera mentioned. Even in a chaotic world what the top dog says is law after all, maybe a MC with low corruption and high morality?
Slight correction. Monsters are needed to make superhumans. If there was no monsters at all, superhumans wouldn't exist. The pills Ella uses is a lure for compatible types to come and infect their new spawn. There's 2 known ways to become a superhuman. By being directly infected by the monster(MC, Deryl, Michael, Demi, Valravn) or coming in contact with monster parts and corpses(Tiffany and Alice partially since the Fairy was comatose). Both ways still require for monsters to exist, which is also part of the problem. As long as monsters exist, so will superhumans. Killing all superhumans or letting them reproduce would actually make it easier for monsters to wipe out or convert all of humanity, with what we know currently.
As we learned this update. Humanity as it is would struggle against C Class monsters and a B Rank monster can't be beaten by them at all with A Rank being able to wipe out an entire sector(s).
In case anyone forgot the equivalence for the ranks:
Rank S = Level 5 Superhuman(s) needed
Rank A = Level 4/5 Superhuman(s) needed
Rank B = Level 3 Superhuman(s) needed
Rank C = Level 2 Superhuman needed
Rank D and Below = Level 1 Superhuman needed
So basically, humans would get wiped out by rank C and B monsters, monsters that are only around lvl 2 to 3, if you took away superhumans. They also probably make up the abundant amount of monsters, number wise, so groups of them would fuck up the world. Add a single A rank and that's it, let alone S Rank.
So yeah, limiting superhumans would basically be a extinction lvl decision. It's already hard to reach lvl 3 as a superhuman, let alone 4 and 5. Without any at all, humanity gets destroyed by B Rank monsters and their hordes below. This also doesn't even factor in that the monsters can reproduce with each other and infect other species, including animals(see Valravn). Humanity would be completely screwed and to be frank, there's no real great ending for them in this all.