But if she were part of the X-team in the future, how could she possibly be cut? It seems impossible that she would've been a part of those fight scenes and then... not.

You'd think so, but Arwen was actually in Helm's Deep, i.e. Liv Tyler did film several battle scenes, before they decided not to go there in The Two Towers and pixelled her out of all the battle scenes she's in. That being said, my guess would be that Rogue does early on in the future, yes, not least because it would add poignancy to Wolverine seeing her alive and well at the end. As for Anna Paquin's place in the credits, again, see Liv Tyler in the LotR movies where she got one very high up there - I think she was fourth or fifth named - which in no way reflects the amount of her actual screentime. If you have a good agent and a good current Hollywood standing...

They should've told Mystique, "shooting Trask will result in X3!"

But then she'd gone with Charles or Erik immediately and it would have been a much shorter movie. :)

This may be the first time that a time-travel movie actually fixed continuity.

No kidding. BTW not having watched the two Wolvie solos I wouldn't know what happened in them anyway...