So a mission builder is going to be in the game (at some point) that, as far as I know, has been said. But I'd like a smaller version for bases.
It'd be a room in the base (or console or what have you) that would allow you to run combat simulations. So just a simple room for testing out powers, teaming, builds, etc.
Another neat idea for this (or the mission builder in general) would be that you can only use enemies that you've defeated before. Going to bring a new team to fight a big boss you've faced before? Bring them into this place so they can learn the fight. Could even have it simulate entire boss rooms.
Like the danger room of the x men to use an example a lot of people would know.
"Let the past die. Kill it if you have to."