Not saying manipulating people is good, but I'm pretty cautious about labelling people evil, and we still don't know what Ella's endgame is. So long as it's a good outcome (edit: i.e. goal), I don't think you can unequivocally call her evil. I generally reserve that for people who have negative goals, like genocide, or neutral goals that they reach through negative means, like serial killing (the goal is pleasure).
There's no reason to think Jake would have fucked up Daryl's brain the way he did Mia. That only happened because of the stress of Mia finding out his secret and deciding to tell the MC.
She didn't use Mia as a hostage, she used her as a bargaining chip. Ella will fix Jake's mistake if Jake does what she wants. She isn't threatening to harm Mia, just to not help her, and she's under no obligation to help Mia.
The goal itself as well as the way of achieving it contributes to the standing of the person. If either is just straight up evil, then you by the very definition cannot be a good person, and being "neutral at best" is very debatable, as traits that can be shown as positive do not contribute to the overall distinction (example: caring, protecting and being loving husband to one's wife, or any person from one's family, does not make one good, an astonishing amount of mafia guys from all around the world are great examples of that). People are complex, have many different parts and angles to them, and one can have good goals and still be fucking evil, just forced to behave ina a way, and vice versa.
We can, tho, look at what a person does when it has a choice, is not forced to anything and make that distinction. If a person does shitty, self-centered, bitchy things to someone else just because, for the power trip, for getting hard over it or any other, then it's evil. Like Ella. She:
- Made people into superhumans that were not able to handle it one way or the other, that then monsterified. That is killing a person over own's self ego. If monsterification is not considered killing, then Jock#2 was killed by her personally. That is evil, straight up. Her not arranging infection of Emily, because she was worried about her pulling through, is not an indication of her being good - if it were, she wouldn't do this shit with someone else.
- Uses people. Like tools. She keeps many with manipulation and lies, she mindfucks into obedience hundreds of monsters (and people) by using other superhuman's powers, has an orphanage for growing useful tools, whose she can dispose of without much fuss if something goes wrong, and when she sees personal gain she does not hesitate to end someone in a flash (see dead end with telling her too much, or being too strong), even if allegedly harboring some positive feelings for them.
- She has a plan, that she works to fulfilling. We do not know what this plan is. But it involves fucking over the world and everyone on it, ensuring somewhere around hundreds of milions casualties at the very best (not all can become superhuman, straight up). And oh so fucking funny thing is - it don't need to work. Ella is not omniscience, she does not know all. Maybe 20 something level fives with a spear made of pure clownium is enough to protect humanity. She does not know, she never reached out to H.E.R.O., or anyone really, to talk this through, going headfirst into what she probably dones't even understand fully, dooming others, even if there are possible better alternatives. Even if she is working for "greater good" (kek), this is evil. Why? She does not check, her ego as the only one that is right. If she would care for common people's lives she would expend even the most basic amount of effort to try something that is less lethal, and she made a choice to do fuck all int that regard.
-She behaves as self-entitled, self-centered, self-absorbed, narcisstic cunt. To everyone she can, or think she can get away with. Power tripping is not a good thing, neither neutral too.
Among many others. in short: Ella is evil.
The MC isn't dumb, he just doesn't think, which ultimately stems from his apathy. It's not that he can't put the pieces together, he just doesn't feel like it.
It is funny concept to me, the evolution rebuilding your body, making it so insanely better. Except the brain, brain is not a part of the body, as evident by MC, or any superhuman really. Level 5's should have supercomputer level computing powers and just about perfect memory judging by how their bodies develop in contrast. Even one level should make average MC excell at school stuff with no effort, but he did not improve in that regard.