You make some good points, but I have a couple of my own.
1) Nightcrawler was super badass in the first scene.
I'd say that under the effects of the brain-juice, Nightcrawler was free to express all of his repressed badassedness. I also assumed it was a big fat jolt of fearlessness.
2) Magneto giggling like a school girl at Rogue on the plane.
Dude, I really thought that was funny. This one of the most powerful men on the planet, taking time out of his busy genocidal schedule to mock a little girl. That was a really cool character moment for me: it's easy to set up a character as an 'evil genius', but to make him catty, petty and puerile? Genius.
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'll cheerfully concede that.
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.
Exactly. It's not like Lady Deathstrike would pose much of a problem to old Magnus. Just kill everyone inside, set Xavier to 'kill bot' and be home before General Hospital.
7) The worst scene of the movie was the Jean Grey death scene.
Eh. I didn't have a problem with it...mainly because I thought the reason she left the ship was because her powers were interfering with electronics (um, except for the dogfight earlier---but shhhhh). I was hoping that the engines would start up once she left the area (which would prove my hypothesis), but I *hated* the fact that she turned them on via remote control. Point conceded.
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).
Again, I think he was acting with doped-up, reckless abandon in the opening. No problem there.
But yeah, it's pretty safe to assume that the two feet in front of a door is probably clear. Lame excuse for a callback to the Storm/Kurt 'faith' moment.
11) Wolverine could smell who Mystique was in the last movie. Why not this one?
I wracked by brains to come up with a counter to this, but all I could come up with is Hugh Jackman really lobbied hard for some 'grind-time' with Famke Janssen.
I don't blame him.
12) In the plane chase scene Magneto sealed up the blackbird. When they were flying back to Washington, the hole came back. I thought that was an appropriate analogy for the whole movie.
Great line

, but no dice. I just checked it out: while the plane is pretty banged up, there is no hole in the return trip. It ain't pretty, but it's sealed.
I mean, if there was a big, gaping hole in the plane, wouldn't Scott have jumped out of it?
Sorry.
edit: me no talk so good.