It feels different because it's a different creative team, so there is inevitably going to be a different feel.
But overall, yes, I do feel that it maintains a very consistant tone.
X2 ended with the X-Men making a challenge to the President; "We are being given a moment, a moment to repeat the mistakes of the past, or to work together for a better future. We're here to stay, Mr. President. The next move is your's"
X-Men: The Last Stand opens right up, showing us exactly what came of that challenge; mutants obviously weren't blamed for the events of X2, since there is now a mutant-friendly presidency, with an entire department dealing with mutant affairs, a mutant in the cabinet, etc...
X2 ended with Wolverine making his choice, finding a new home with the X-Men, telling Stryker "I'll take my chances with him". When we open, we see him as a regular, valuable member of the team, training with them in the Danger Room.
I watched X2 the other night, and a lot of people who find it neccesary to hate on X-Men: The Last Stand will say that what happened with that movie ruins X2 for them. For me, it was just the opposite. For me, I was able to appreciate certain moments even more, because I was able to see how they played out. For instance: "Ever since Liberty Island, you've been different. You used to have to concentrate to levitate a chair or a book, now when you have a nightmare, the entire bedroom shakes" We see this in the infirmary scene between Jean and Wolverine, when her emotions take over and the entire room... shakes. The challenge made by Xavier to the President, we see how that plays out with a pro-mutant administration. And yes, I even find the arc they took with Phoenix to be very much in line with what Singer set up. It might not have been what Singer was setting up, but it definatley fits in with what Singer had already established.
Magneto is very much the same Magneto, holding true to his promise at the end of X-Men: "The war is still coming Charles, and I intend to fight it, every step of the way, by any means neccesary", and indeed, that is exactly what he did in X-Men: The Last Stand, fight that war by any means neccesary.
The fact that I highly enjoy this movie is no secret around here. As much as I love this film, I still find myself with many complaints about the film. The consistancy to Singer's films is NOT one of them. To the point that I truly feel that anyone who states that it is -not- consistant with Singer's films, they are just looking for something to complain about because it's not a Singer film.
No, it's not the "X-Men 3" we would have gotten if Bryan Singer directed it, but Bryan Singer didn't direct it. So of course it's a different movie. He left, and he took the ENTIRE CREATIVE TEAM with him to Superman Returns; script writers, composers, costume designers, EVERYONE went with him. It was a totally different team on this film, so of course it's not going to be a carbon copy of what Singer would have done. But it maintains the tone, and consistancy of story, from Bryan Singer's movies, and for that, I applaud Brett Ratner. This is the biggest reason why I am happy we got Brett Ratner, and not Matthew Vaughn. Vaughn made it pretty clear, his feelings towards Singer's films, and those feelings were not feelings of respect. He would say the company line, about how much he enjoyed the films, and in the very same breath, talk down on the movies about how bad they were. Matthew Vaughn would have given us a horrible X-Men film. I know many people have complaints about the film as is, many warranted, many not, but it would have been MUCH worse under Matthew Vaughn. Of that I am certain.