The main differences in the last few years was he was writing X-Men as more sci-fi (with some weird ideas), and depict the X-Men more as political activists rather than superheroes.
Here's a short summary of what happened (there's some spoilers below)....
The school expanded from having about dozen students to having hundreds of students much like the movies. Professor X came out of the closet on being a mutant, and made the X-Men public. The X-Men became international as the X-Corporation having to staff it with second-tier X-team members like Domino, M, and Sunfire. There's a cult of humans running around wanting to become mutants by grafting mutant parts to themselves. The mutant nation of Genosha was wiped out by mega-sentinels.
An entity known as Sublime was behind everything. Most of the time a group of students mainly composed of the Stepford Cuckoos a group of telepathic sisters who took after Emma Frost, Angel Salvadore a part-fly/trailer-trash girl, and Barnell "Beak" Bohusk a Dutch kid who looks like a chicken saved the X-Men many times.The phoenix entity returned and Jean Grey died yet again. Magneto is dead yet again. Weapon X was revealed to actually be Weapon 10, as Weapon XII, XIII, XIV and XV showed out. Prof. X quit as the headmaster of the school, and Emma Frost and Scott Summers who are now a couple are the headmasters of the school.