I think it's a cool idea, for what it's worth. I was actually thinking that, as I read your story post, that you couldn't just let that go there. My vote would be for the New FF (Spidey, Logan, Hulk, Ghost Rider), and also, you mentioned that the Skrulls were going to assume the FF's identities, so you could have the FF on the dark side. (Of course, this game and so many others prove how effective they are, but if you split them up and put them on teams with Doom and the other powerhouses, they could have half a chance of survival.) One bonus of that is, you'd get to have a game where people wouldn't mind seeing the FF get creamed!
I'd watch it.