UGH, I hate it when they take concepts like this, choosing sides and all that. Plus I didn't really like Civil War at all. So this, displeases me
I honestly don't mind.
I mean okay, fine, I enjoyed Civil War... but honestly, these games ---
X-Men Legends,
X-Men Legends II: Rise of Apocalypse and
Marvel: Ultimate Alliance --- have never been really about one single story but about cherry picking as many concepts and stuffing as many characters as possible into one game in an attempt to please the broadest range of fans possible.
To actually nit pick that is utterly beside the point, since from the very beginning the whole point of these games has been to just been a big ole masturbatory sandbox of Marvel characters, which I have generally enjoyed (even if I have a ton of criticisms about them).
I sincerely doubt they're going to construct the game so that you'll be forced to keep Pro-Reg and Anti-Reg heroes apart from each other, since the developers probably want to avoid preventing fans from NOT being able to create line ups of their choice.
Two designs are likely then:
Either the design is going to be about taking the Pro-Reg and Anti-Reg with ONLY Captain America and Iron Man having their affiliations constant, and some characters locked (clearly at some point players will have to fight Thor, for example, even if it means using that ridiculous rubber stomp move that Mr. Fantastic has) if not totally unplayable (like Angel and Beast in XML2) because they have a position in the story. This means that if they're smart they will try to script all the playable characters to have a rationale to be Pro or Anti-Reg.
Or the design will have one master path that may or may not have some branching scenarios and the characters can be unlocked and at some point the sides of the Pro-Reg and Anti-Reg converge so that Human Torch and Iron Man can be playable together or something. I suspect this is most likely, since the developers don't really try to follow existing storylines too closely, and it's probable that this whole Ultimate Alliance Civil War is just a story ruse for a Big Bad who is conspiring to get the heroes to beat on each other, just as the XML2 Apocalypse Age was not an alternate reality but merely a scenario in which Apocalypse really did mount a good shot at taking over the world.