I feel like you are exagerating with the kill count on humans. If he had killed hundreds, he wouldn't be up for negociations with the government, he'd be public enemy #1.
Michael was trained since he was young. Saying the MC has the leg up on him because he fought different targets is akin to saying a guy who's been in a hundred bar brawl is a better fighter than a profesionnal boxer.
There's a vast difference between what the MC does in order to survive, which is closer to flailing around, and the discipline Michael has, forged throughout over a decade. Sure the MC might have more hands on experiences with monsters and superhumans, but Michael has the basis to progress far faster than the MC on that front (and to be clear, I'm not talking Power and evolution, I'm talking purely on fighting efficiency).
It's still something he can learn to manage. For example, fire was way more dangerous for him until he learned to somewhat protect himself. It's not foolproof, but at least he doesn't get it as bad as before.
Yeah Michael's combat sense is insane, even just from the perspective of tactics, he can probably figure things out way better than the MC. He is superior to MC in every way I can think of except his powers, but now that he has his own, he is going to become a beast. He just needs to overcome the initial hurdle of learning what they are and how to use them, playing catch up, and that's it.