I'd like to see at least an attempt made at continuity with X1 and X2; but it would make me very, very happy if they just scrapped X3 altogether and said it was a bad dream and tried again for a grand finale. Same with any continuity references to Wolverine.
As far as Jean and Scott being teenagers --- that continuity is already shot, since they made Jean Grey into a 30-something milf while Cyke was still in his, say, mid-20s. That would put Jean's teen years in the 80s and Scott's in the 90s.
Even though Halle Berry and Alan Cummings may have been fairly young when they took on their roles, both Storm and Nightcrawler are "ageless" enough to get away with putting them in a 70s (or even 60s) sequel (prequel...er, tween-quel...???). You might even get away with that for Colossus, and say something about the steelskin mutation slowing down his human skin's aging process.
In fact, I'd almost demand to see Nightcrawler in XMFC2. Have Azazel and Mystique hook up and Raven give birth to Kurt, and you've (finally) established a continuity that actually *agrees* with the comics for once.
Other than that, I'd like to see them introduce some of the also-rans who haven't really appeared in 70s and 80s XMFC sequels....
*Nightcrawler (see above)
*Colossus (ditto)
*Storm (ditto)
*Polaris (she's a natural to become a love interest for Banshee)
*Psylocke
*Gambit
*Jubilee
*Mimic
*Dazzler
*Domino
*Sunfire
*Sage
*Forge
*Thunderbird
*Cannonball and Husk
*Karma
*Wolfsbane
*Dani Moonstar
*Boom-Boom
*Sunspot
I'd also like to see Cable and Bishop come in together from the future, but not in XMFC2....I'd rather hold off on a "Days of Future Past" (so to speak, sorta the way they handled it in one of the animated series) until the third XMFC sequel.