I had the same idea about origins, but I agree that trying to add power customization would be difficult. Though, I do have a suggestion on how it could be done (read #3. below). Anyway, I have 3 ideas on how to make origins actually matter.
1. How about adding certain inherent advantages/disadvantages or buffs/debuffs (whatever you want to call it) to each origin, independent of the archetype and your enhancements.
Example: All toons with mutant origin will have additional toxic damage resistance. All toons with magic origin are more resistant to dark powers.
2. How about dual origins? There would be consequences though. Add my first idea to this one, you would have only half of the advantage/disadvantage (buff/debuff) as a single origin toon. And single origin enhancements wouldn't be as effective for your dual origin toon.
3. How about sub-origins? My most complex, and probably unrealistic idea, but I think it would be cool anyway.
Example: So you do have a magic defender, but you don't want to use a wand with your powers, fine, why not have 3 different sub-origins within the magic origin. Maybe one would be your witch/wizard sub that uses a wand or staff with all powers. A second would be a sorcerer type that doesn't use any wands or objects with their powers, and a third would be magic creatures or something.
The number of sub origins is almost irrelevant, but my point is that whatÂ’s wrong with having a robot toon that sounds and looks like a robot. It wouldn't satisfy everybody, but wouldn't it start to open up the door of possibility of power customization and add to character customization.