Woah, this thread exploded all right. Good stuff, keep them coming.
The way I see it, both HERO and Ella are useful.
HERO provides a (mostly) safe environment to train and make friends, gain some knowledge and access to stuff that wouldn't be easy otherwise. HERO knows a lot of important stuff about how evolutions work, the potential of level 5s, and has a lot of academic knowledge. They have the evolution syrup, know how to work with monster material to make armor, can help weaker superhumans (some of them being the MC's friends), to realize their potential/manage their symptoms. Additionally have quite a few level 5 members that can protect the MC if the worst comes to pass (Nico with her teleportation, Nyx with her Mark) etc. I don't give a shit about eugenics etc. It's not that I approve of the practice and the state of mind that one has to have to do stuff like that, but the truth is that this whole world is built on a blatant abuse of power. Humanity never stood a chance against MCORP and they won't stand a chance against HERO too. Perhaps if the MC ascends he may get the chance to change the status quo, but for now it's just irrelevant.
Ella on the other hand provides the Battleground and the growth. HERO is a fairly sterile environment. It's only when Ella gets involved that things get interesting. MC will benefit immensely by spending some time with her, seeing her operations, getting acquainted with her monsters and her Superhuman allies that provide the structure of her operation. She knows more about the higher ups of monster hierarchy than HERO and since MC's evolution, it's fairly obvious that he will have to deal with these things. Without Ella, there would be no need to click on the "train" button. If you do however click on it the moment you see it, her trials are fairly easy and she admires you for it (with the exception of the damn deadend).
Considering that it's possible MC will eventually reach the very top of the food chain, I don't really see these 2 as opposites. The way I play the MC, he shows as much loyalty as needed to retain the ability to stay involved. I'd rather play both sides and get as strong as possible than choosing based on who I think slighted me more, especially if their intentions are not to bring me harm.
My opinions on some of the characters:
About Jake:
He was a kid that had it rough. When he got his powers, he tried to use them for some questionable things but his conscience eventually got the better of him. Ella overestimated him and went overboard which broke him. She also leaned way too hard in his fuckup with Mia (which wasn't intentional, it happened during his evolution). He did fuck things up too much during the last fight, using humans against the MC, but it's obvious that he still is apologetic and willing to accept his punishment. I don't mind him. I think he still has the potential to be a valuable ally, but his growth is stunted.
About Nico:
The problem with this chick is that she is unreliable as fuck. She fights for personal reasons and likes to overextend, she makes whimsical decisions and doesn't follow through with her assurances. She acts like a traumatized little girl that just got her power (which is quite possible she is, after all past level 4, the body changes and it's impossible to tell her age). This isn't someone that I want having my back. I don't mind her antics, but at the moment I consider her one of the weakest characters and she needs to grow.
About Cole:
The idiot bully. I don't know the circumstances that made him that way, but he managed to paint Ella's operation in a much more negative light than all the collateral deaths she caused could do. He also talks a big game but to me it seems like he has some inferiority complex and he tries hard to prove himself. I think the perfect scenario would be for the MC to fight and beat him as a level 3 vs level 4 fight but I can also think of a lot other (and extremely perverted) ways to punish him. I don't care too much about killing the little shit. I'd rather have him finally admit his place. He actually seems loyal (even if unreliable) and his concern for Ella shows that he isn't a total lost case.
About Charlie:
Seeing her stand with Jared was painful. I don't buy the argument that she saved us. Jared couldn't even break MC's skin with a cheapshot while both MC and Alice punch way above their weight class. Right now she is in my shit list and I hope that she had a reason for meddling. This wasn't just a random encounter. She was part of a group that killed a friend in cold blood, her brother was part of a group that directly antagonized the MC, she is part of Ella's group which is the aggressor even if she has reasons to. No matter how good she was to monster Deryl, she has exhausted all goodwill. I won't yet go murderhobo on her but she better avoid fighting me.
About Xanthe:
The old man has a lot of game. I find his behavior refreshing. He is weirdly upfront, he doesn't back down from his plans no matter what, and he is a curious scientist who is perfectly fine with giving us more power just to make some observations. Now of course, while it doesn't show, he has to be dangerous as fuck. This is not a guy that you mess with.
About MC (and how I play him):
I won't go too in depth here, but the way I play him is a mix of apathy, easygoing behavior and always up for a challenge. While it's possible to play him as a shining beacon of virtue, I think his natural state is being a Neutral. I've chosen to go the Hero route with my vigilante persona, but the drive wasn't to save people, rather to put the MC in a situation where he both has to rise to the challenge and be held accountable for his actions. My MC doesn't care if people die. He cares about doing the best under constraints. He is a lot like Michael in that regard. Not powerhungry but they enjoy combat and becoming their best versions of themselves. Michael is a bit more pure in that regard, while my MC's drive is a mix of curiosity and desire to protect what's his. I'd rather turn people to my side than kill them for example.