Margaret Weiss Productions produced a Marvel-themed Cortex-Plus game in 2012 called Marvel Heroic Roleplaying. It won awards for the system and the game in general, although it was short-lived due to licensing costs.
https://en.wikipedia.org/wiki/...l_Heroic_Roleplaying
I'm fond of the mechanic (thanks to the Firefly game she produced), and, while it's a bit crunchy, it also allows for a great amount of flexibility for powers and has a neat "attribute" mechanic called Affiliation (which basically allows you to choose whether you work best solo, with a buddy, or as part of a team).
The only thing is doesn't really have is a set rule for how powerful your custom-made character can be, although I've come up with something that I think works rather well, based on the example characters from the rules.
That said, it's a bit to learn (and we'd have to convert all the characters), but I figured I'd throw it out there as an option.