Assuming the game still uses an origin system, allow for people to choose the origins of their powers individually. Have the main origin they choose be the default, but let them change some powers to have different origins.

Heroes (and villains) can have long, exciting careers and gain many new powers as time goes on, both in games and in comics. But sometimes those powers don't quite fit with the character's original theme. For example, maybe the character is a mutant who has the power to throw fire around, but those powers don't let him fly. Instead, he uses a flight belt invented by one of his close friends that lets him get around. So that would make his travel power as technology origin, instead of a mutant origin.

And, let's say that the character's natural powers hit a peak at some point. But in his travels he finds an artifact that unlocks even greater powers, so long as he's wearing it. So his low level fire powers are all still mutant origin, but his higher level ones switch to being magic origin. There are countless other examples to think of, too.

I'm not sure how Origins will be used in this game, or if they'll be used at all. Whether they'll have gameplay implications, or just be RP fluff. But either way, I'd really like to be able to customize the origin of my character's powers a bit. I think it would be one of those little things that adds a bit to the game... not used by everyone, but really appreciated by the ones who do use it.