About as much sense as Magneto planting a machine at the top of the Statue of Liberty--during which they did drive up in a boat, which Sabertooth promptly landed on when he fell from the Statue. How does he escape from that?"
Magneto can Fly can't he. He can fly and move metal at the same time can't he. Was it impossible for Magneto to use his powers to transport the machine up to the top of the statue of liberty? If Magneto did this in broad daylight I would agree with you. But, he didn't and he had his mutants kill all the people who were guarding the statue.
Who said Sabertooth survived? We never see him again do we.
"He destroys the whole complex in one shot, what happens to the battle sequence. I'm sure many of these stories would have made more sense if the bad guy simply annihilated the competiton."
I guess this can all be explained because in X-Men 3 magneto is older and became senile. Therefore he lacks the inteligence to come up with a great scheme for attacking Al-Catraz.
"I'm sorry if this comes as a small consolation." He was willing to kill Rogue because he wasn't willing to sacrifice himself, which Wolverine pointed out that if he was so righteous, he would have put himself in the machine. He could care less what happened to Rogue, as long as he got what he wanted."
But, he did not truely want to kill Rogue. He believed her sacrifice was for the greater good of all mutants and humans. In X-Men 3 there was no indication he gave killing Leech a second thought. There is a big difference in Magneto's attitude for these two films.
"In X2, he left the X-Men behind while he and Mystique (and Pyro) left in the helicopter. He knew that the dam was about to break."
This is not true. There was not one scene in X2 that convinced me he knew the damn would break. It that was true why did he go through all that trouble to change the settings in Cerebro 2, knowing his plan to kill all humans would not work due to Xavier drowning.
"He left Mystique after she was cured. He was about to kill Wolverine before Beast cured him. He "let the pawns go first" in the first wave of battle."
Which is why I did not like Magneto in X-Men 3 because he acted out of character too many times.
"He doesn't have a problem killing Leech."
See above answer.