Yeah, that is one of the things that really appeals to me about Mutants and Mastermind's design philosophy--you do not get character generation resources for taking flaws, but rather you get resources in play when they come up. Though it does seem more common to use the get immediate payout like we see here in Dungeons the Dragoning

Looking forward to the magic chapter. I was looking at spells, but without experience with the system, it is hard to judge them.