Joker, you're cracking me up. I never knew you were this much of a comic fan.
I'm sure you probably saw where I mentioned it, but there was an interview with Brett Ratner (who directed X3), and he basically said that while Bryan Singer (director of 1 and 2) was a huge fan and tried to stick to much of the storyline of the comics, he (Ratner) basically just skimmed through and grabbed all the stuff he though looked cool.
I think the reason they never make much effort to stick too closely to the comic is that the structure of a film is simply different than that of a comic book, or series of comic books. I have no clue how long the average comic storyline will last (it's been years since I've read one), but most movies, or pretty much all Hollywood movies, stick very closely to a 3-act formula that's basically:
1) situation is introduced
2) conflict is introduced
3) conflict is resolved
As someone who's read a lot about screenwriting, I've read a lot of stuff about how most studios actually make their writers adhere very, very closely to this formula, to the point that each script must be 90 pages (1 page = one minute of screentime) and the second act must clearly start on page thirty, third must clearly start on pg sixty. It's just as mass-produced as any fast food. And it sucks that so many potentially great stories get screwed over by this formula.