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How about a prequel? Focus on how he got to the point where he is now. Like 'Breaking Bad': he starts out as a complete underdog and quite sympathetic, and everybody roots for him - and gradually he grows more and more powerful and less and less human until he is a complete monster. Say he didn't do all of this alone. Say Prometheus started as an organization that resisted Chronos from within (Kind of fitting, since Prometheus opposed Zeus), like professor Odagiri, and gradually they all sacrificed themselves - until Strigoi betrayed the last of them, using as an excuse that this would gain him enough power to defeat Chronos for good, in a perfect Pyrrhic victory: by now, he was as bad as the thing he was fighting.

My advice would mirror what Salkafar has said. While it is tempting to make your main character uber powerful it actually limits the use of the character in your story. Simply put the more powerful the character is the less you can actually use it as he / she will simply overkill the opposite side of your story (whomever is the foe). You can easily end up in a situation were your main character ends up taking a more minor roll later in your fiction if you're trying to flesh it out and explain plot points but your character is killing off every other character so quickly the plot just disappears. Saying that, if your intention is just to have your character stomp over everything and simply win it gets boring very fast. You should always find ways to screw over your character and give it weakness. e.g. One Punch Man wins so easily he's bored. But that is more satire than sci-fi but if your character isn't human and has human flaws it'll suck. Making him the Brainiac of Guyver / Halo sounds more like something you should do to a characters rival than to your main character. No one can do anything by themselves, I'd personal split your development between 2 people, either brothers or best since childhood friends and give Prometheus to hero and have the Brainiac of the two everything else in terms of skill set who warps to be the "villain" of the story. He does crazy drenn like turn Chronos into a Creator / Engineer army and your hero has to stop him. You can fill Prometheus then with all sorts of rage because he would feel personally responsible for his friend / partner being what he is even if mentally he is the weaker of the two.

....That is an interesting thought. Does Archanfel know the names of all the Zoanoid types? I am gonna say 'yes', he knows all about all of their qualities. After all, he's the one who has to deploy them. In fact that's probably pretty much all he knows. So are all the Zoanoid names originally made up by the Creators?? They are all alien words? Now I feel even more justified in making this thread.