>3) The whole break-in to the base. They had Magneto with them, and then they launch this complicated plan to attack a base mostly made out of metal.<
I had the same thought the first time I saw it, and still largely agree with this idea. However, perhaps the reason they needed the X-Men was not so much to get into the base, but because they needed to do something about the soldiers? Remember that Magneto was completely preoccupied while "fixing" Cerebro, and that if the two of them were alone, Mystique would have been the only one who could have held off Stryker, Deathstrike, and the soldiers. Even if they had managed to take out most of them, they had no real way of knowing if they got all the soldiers before they attempted the reprogramming, and time was of the essence.
>5) For that matter, why didn't Magneto and Mystique just steal the jet and go themselves? They didn't need any help, and bringing the others along is just asking to get thwarted.<
Again, see above. Seems like the most logical reason to me, the more I think about it.
>9) At the beginning of the movie, and on the plane, Nightcrawler had no problem teleporting where he couldn't see (too accurately for my taste, actually). At the end, he was scared he would run into something when he was about to teleport through a door. Last time I checked, most people don't build walls on the other sides of doors.<
As for the White House, Stryker could very well have supplied him with a (mental or physical) map of the place, so that he knew where he was going, not to mention that he didn't have all that many qualms about what he was doing in his programmed state. As far as the plane... I agree with you...
>11) Wolverine could smell who Mystique was in the last movie. Why not this one?<
I don't think it was so much that he smelled her specifically, just that he smelled someone *in addition to* the other X-Men at liberty island.
Now why he wouldn't remember her scent... I had the same thought, actually.