I say Proteus. Its probably the second best X-story ever. X4 should take place about a year or a year and a half after X3.
Main team: Rogue, Iceman, Colossus, Angel, Shadowcat, Jubilee, Wolverine, and Gambit and Psylocke.
Storm, Jean, Cyclops, and Beast are just teachers now. With Rogue, Iceman, Colossus, and Kitty all in college (somehow through Xavier so they can still be X-Men) to become teachers. Wolverine of course is still there. Hopefully Gambit will at least cameo in X3, so his backstory wont have to be told. Psylocke is with STRIKE and thats where we meet her.
Since Moira is in X3 (supposedly) hopefully we'll get a glimpse of Muir Island and that can set us up for X4. Id go with a combo of the Ultimate and the 616 versions of Proteus. He should be Xavier's son, I think. That way we get more story. The X-Men go to Muir Island after Moira's call, find Kevin is lose, and contact STRIKE (or they could just call it SHIELD.) Professor knows of a young powerful telepathic mutant (Psylocke) and tries his best to find her. She is the head of STRIKEs Psi division (Britain being the first country to realize mutant's potential for good) Anyway she agrees to help, big ole fights happen, cameo's are made, Professor eventually gets desperate and contacts Magneto and his Brotherhood for help, they refuse saying they have 'bigger' problems (the US Gov is beginning Project: Apocalypse (Sentinals), thereby setting up an X5) anyway Prof contacts his 'retired X-Men' Cyke, Jean, Beats, and Storm, who come and all together the save the day. Psylocke eventually agrees to move to America to join the X-Men. Leaving the X-Men as follows: Wolverine (leader, its bound to happen), Rogue (co-leader, hey she's been there longest), Iceman, Colossus, Angel, Shadowcat, Jubilee, Gambit, and Psylocke. With the 'elder' X-Men being: Cyclops, Jean (hey when are they gonna get married in the movie-verse? hmmmm??), Beast, and Storm....and of course Prof X.