Overall, the first two films were pretty decent, the only changes I would make are more for setting up the third film, trying to ease into Sentinels and the Cure, and getting as far away from mystical Phoenix split-personalities as possible. If people like some of the changes, I'll flesh them out a bit and post some ideas for the third movie. I picked up ideas from everywhere, so don't be too judgemental about it not sticking with the comics.
X-Men - Similar to Singer's, with minor adjustments
X-Men:
Cyclops - A militaristic tactician and skilled fighter, not a lost puppy
Jean Grey
Storm
Wolverine
Brotherhood:
Magneto
Mystique - Hints that she and Magneto might be a couple.
Sabretooth
Toad
Rogue - A timid, uninitiated member of the Brotherhood who changes sides when the Brotherhood abandons her at the end
Junior X-Men (Glorified Cameos):
Iceman - Introduced as a tour guide/love interest for Rogue
Pyro - Leaves the school at the end
Shadowcat
Jubilee
X2 - Also similar to Singer's, but with further setup for a more grounded X3
X-Men:
Cyclops
Jean Grey - "Dies" the same way, but does not return until the very last scene of X3
Storm
Wolverine
Brotherhood:
Magneto
Mystique
Pyro - Protege to Magneto, makes Mystique jealous
Government: All advisors and administrators of various degress
William Stryker - Secretary of Defense, dismissed for events in the first movie, becomes religiously opposed to mutants.
Nathaniel "Sinister" Essex - Pushing for genetic testing of mutants, secretly manipulating his own genes.
Remy LeBeau - Underling of Essex, similar to Deathstrike's role
Bolivar Trask - Pushing for eradication through SWAT enforcers codenamed Sentinels
Junior (Honorary) X-Men:
Iceman - Slowly becoming a team leader
Rogue - Crush on Bobby is dashed due to a number of reasons, later comments on Gambit
Colossus - Portrayed as a 22-ish (as opposed to the 16-17 of the others), quiet, Russian farmboy
Shadowcat and Jubilee - Similar characters, with Shadowcat being a little more girl-next-door and Jubilee being characterized as, ... well, Jubilee, who calls "dibs" on Piotr, but doesn't get him
Nightcrawler - Introduced the same, or very similar, but including a scene at the end where he converses with Xavier about the overall violent nature of the school. Receives a uniform and communicator in case he or the X-Men need help, and is sent to Moira MacTaggert in Scotland.
Edit: Technically, shouldn't this be moved to the X-Movies section? Although, I don't blame Spider-Kurt for putting it here, that section of the boards gets scary.