Wolverine: "I think she killed Scott."
Xavier: "Look what happened to Scott. You killed the man you loved because you couldn't control it."
Wolverine: "We lost
Scott. We lost the Professor..."
I hate the "direction" they took with Cyclops just as much as anyone, but no, he was not forgotten about.
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To answer the question, by far,
X-Men: The Last Stand.
X-Men 3 is not a bad movie. Not in the least bit. It's probably my favorite
X-Men movie.
Singer's movies were great, and
X-Men 2 is definitely better than the first. Singer's movies were great for showing us who these characters were. But what they were weak on was showing us what these characters were capable of.
X-Men 3 was the X-Men in action. All the development was done in the 1st 2 films, so while this movie would have benefited from a little bit more character focus (particularly Jean and Angel), we've already had 2 movies where we learned about these characters, their motives, their relationships, etc...
X-Men Origins: Wolverine just doesn't measure up. The characters aren't as good (no, it's not because they were poorly developed. It's because Kayla Silverfox can't hold a candle to Jean Grey. William Stryker is no Magneto - although Stryker is a good villian. Agent Zero, John Wraith, they are no Mystique, or Beast. I just really don't feel the same attachment to these characters as I do the
X-Men characters.)
The story in
X-Men 3 is more powerful to me, more epic, more emotionally charged. The characters in
X-Men 3 are more beloved (my hype for
X-Men Origins: Wolverine wouldn't be nearly as much if it weren't for Gambit, Cyclops, Emma Frost, Xavier...) than those in
Wolverine.
I think the ONLY thing that
Wolverine has on
X-Men 3 are the individual fight scenes. The Logan vs. Creed fights in this film (all 3 of 'em), Logan vs. Gambit, Zero and the helicopter vs. Logan, these are the best fights in the entire series as far as I'm concerned. Wolverine vs. Sabretooth, Wolverine vs. Mystique (
X-Men), Wolverine vs. Lady Deathstrike, those fights were way too overly choreographed and unrealistic in my view. Wolverine didn't really have a 1v1 battle in
X-Men 3, though the fight sequence in Jean's house, and Wolverine's rumble in the woods are both badass (same with Wolverine's rage in the mansion in
X2), but Wolverine vs. regenerating arm dude was really cheesy.
Overall,
X-Men 3 is just clearly the better movie in my book. I still think that it's probably the best of the entire series. The action and epic story sequences in
X-Men 3 build off of the development and depth of
X-Men and
X2 to finally showcase the capabilities of these characters in epic, emotional fashion.