Okay. Let's see how this answer turns out...
I'd like for all of the characters to be weak, if not a little clumsy with their powers at first. There will be "classes" or training sessions where the characters will learn how to do new things or control their existing powers. No one should be able to do serious damage during the beginning of this RP, so it will more closely resemble, as you said, a skill tree. Later on, who knows? But a key thing that I would like to keep in the forefront is that "Dangerous" malfunctions are terminated. If there are some life threatening powers/tendencies, they should be kept secret from "the man." :P 
I hope that was an okay answer...