I really wanted to like this movie as I'm a superhero movie fan! The problem occurred to me around midway through the movie. The acting was good, the Asian influences were fun, the snaky female villian who changed skins and costumes to signal that the climax was coming just made me go "huh", and I didn't even mind the Jean Grey she's-my-inner-voice scenes. My problem came from the design of the script itself. It seemed like the further along the movie went, the more we were asked to accept and the less sense it made. Yeah, I said it! Characters were angry at one another and trying to kill each other for some pretty "stretchy" reasons and then the introduction of the samarai warrior made out of adamantium complete with drills and cuff locks pushed my envelope over the edge.
I think that the basis for the story ideas and plot points may have worked well in a comic book format but simply didn't translate well to the screen. What we're willing to accept in word balloons and colored art panels falls flat when we're asked to accept it as plausible on the big screen. I know, I know, as I'm typing this I'm saying "Oh come on, you accept that Wolverine exists in a universe but then you can't accept any more than that?" Yep, that's what I'm saying.
At one point Hugh Jackman's forehead, which was furrowed during the entire movie, seemed to be agreeing with me. It seemed to be saying "Can you believe how far we're pushing this? I mean really!"
P.S. I'd like to leave comparisons to the first Iron Man movie and it's robotic villian out of this but to say "Really, could we please take our far fetched climaxes in a fresh direction next summer?"