Alternate Modes?

I'm wondering if there's any plans for things like a challenges mode for villains (things like the one houserule that the Ennead's cards activate all their triggers), a Freedom Six fight vs. Iron Legacy, or things like using all three generations of Legacy? Or some kind of 'make your own scenario' program along those lines?

I think it'd be neat. And also that Greatest, Finest and young Legacy would make a devastating team together.

We plan to add the official villain challenges to the game at some point.

There are no plans to support house rules like the other things you mention. They break the game in various ways, which is feasible to deal with on the tabletop but not in a computer program.