I've read through all the post and a two things popped into my head, just wanted to share them with you.
1. He has very complex and very destructive powers, how does he learn to control them at first, wouldn't he just accidently blow up something before he understands his own powers? You have a lot of possibilities in this case, like when his powers are unlocked he can sense energy in all of its forms but it is very hard to handle a new sense so he panics and flees to a relatively low energy place (wasteland?) where he learns to control it. Might make him OP but you could limit him in other ways. Because I think there are some very interesting possibilities with a sense like that. But apart from the new sense you can do all lot of things with the discovery of its powers.
2. Just a little idea for a bad guy, bad guy is part of the new blood/evolution project too, could be second generation as well, maybe first I'll leave that to you, the bad guy is overall not as good in all aspects of energy manipulation, but he can infuse other people with energy, which has healing effects and makes them physically stronger, he could have a whole cult around him of people who think he is a god that descended from heaven, his primary goal could be to expand his cult (which is quite easy because the people are desperate and he has healing powers) but the cult has some evil cleansing the world idea or something like that, so the hero must stop the cult. When the bad guy heals people he obviously must get his enrgy from something else, but he could use thing like electricity wires or simply a small fire and stuff like that. You can even have a big epic battle where the bad guy discovers that with enough energy he can raise the dead for a short while and he could drain the energy of a power plant to create a zombie army out of a cemetary. Lots of options.
Sorry for such a big piece of text, tell me what you think of it.