I don't see why the changes and characters being killed off make people so dissapointed. Given that there seem to be five or six completely different storylines sharing characters at any given moment in ANY Marvel comic, and given that the overall canonic continuity of the Marvelverse is about as twisted as a dozen broken slinkies in a washing machine, I'm finding it a little ridiculous that people are kicking up such a fuss over stuff like this.
Wether or not The Juggernaut was originally something other than a mutant is besides the point. His presence was desired in the movie, so the empirical concept behind the character - big, muscly, helmet, unstoppable - was taken, the stuff that would have taken an entire movie of its own to explain was scrapped in favour of a simpler explanation that wouldn't screw over the narrative flow of the film.
Main characters dying? So what? [NON-XMEN FILM SPOILER - HIGHLIGHT TO VIEW] It happened to Wash in "Serenity", and I've yet to hear anyone call THAT a bad film. Main characters do get killed off from time to time. In this case, it was done for dramatic effect, and I thought it was effective.
I suppose that if you're a true X-Men nerd, then some of the changes made for the films would be irritating, but the films exist in a narrative set apart from the "core" Marvelverse anyway, and have, in my opinion, greater licence to take things in their own direction - new character concepts, tweaked powers and histories, whatever else. Nevertheless, I think that the essence of what defines X-Men was left intact - sexy people doing cool things, with a few undercurrents about adolescence and racism thrown in.
All the other stuff is just trimming, really.
I say it's time to drop the comic book nerd pretension, and realise that The Last Stand is actually a really enjoyable film that was made very well. The only problems that people usually raise concerning the X-Men films is that they break with canon - but the films never claimed to be canonical anyway, and even then the X-Men canon has looped back and forth through time so often, with characters rising, falling, and being reinvented almost constantly, that it's damned near impossible to say what is and isn't canon anyway.
So can we please lay off with the comic snobbery? A little is fine, but there's such a thing as TOO MUCH.