FCs villains can be apped, but they'd never 'advance' in the system, by earning XP. They would also provide gear for stat boosts to OCs present at a scene when they were knocked out in terms of their HP, in addition to heroes taken out of the temp locker providing the same gear boosts. I've got three levels for temp heroes, six levels for OCs to advance, and four levels for FC villains within the OC ranks to be statted with.
The entire system is sketched up on a Dropbox link, which is the proposition (it's a work in progress).
https://www.dropbox.com/s/1l29l86ob0i173w/villains united system.txt?dl=0
I'm working on extracting the necessary characters and locations for a roster and grid schematic right now.
It should be noted that the provision about heroes as they pertain to your IC power level rank isn't necessarily the 'encounter' hero's level, just the level you need to control it. That way we don't have a newbie running around as Ganthet, unless you've apped for an FC and pass muster through the app process. (I'm thinking e-mail for an FC, on-server chargen for an OC). But, if you got your XP up as an OC, you could have a support character out, like Bullock or Lois Lane.