Seriously. It was done perfectly.
I'm re-reading it right now and the whole thing is incredibly good. I love every second of it, but especially the whole thing with Cassandra Nova, which was brilliant, and the last quarter of the story (where they go to Breakworld).
The part where they are all on the ship talking about how Scott is going to sacrifice himself and setting up the "real" plan telepathically - I love it.
Whedon's run is one of the best examples I've ever seen in comics of a writer writing different characters with their own unique voice. I don't believe that anyone else does it as strongly in this day and age, and it's not just Bendis that's downright bad at it.
But what he's BEST at is misdirection. Things are so subtle and then turned around in such a surprising manner; the whole book is full of surprises.
And the whole redemption of Scott Summers is just awesome. I used to hate Scott; Morrison made me understand him but Whedon made me respect him. He's fantastic through the whole story. So is Emma. And Kitty. Everyone. It's great and this Omnibus is one of my favorite books ever. 9.8/10.
I liked Morrison's run better because of how it changed the X-Men, but it had it's down moments and some of it was hard to understand. Whedon's run is brilliant beginning to end.