First off - excellent movie. Go see it, now. If you haven't seen the first one, I suggest you rent that one to watch first - you'll enjoy the story a lot more. "X2" is to "X-Men" just as "The Empire Strikes Back" is to "Star Wars". A sequel that not only expands upon the first but introduces a whole new story with a gripping cliffhanger ending, complete with a tragic loss (Luke's hand versus... you'll see). Now, I'm an old-school Xmen comic fan, so I'll pop in to answer a few questions and clear things up.
Mastermind was a more imposing character in the comics.
Well, yeah, up until he died from the Legacy virus. But that's another matter altogether. And thanks for pointing out that Mastermind was Jason Wyngarde. I sat in the theatre thinking "Jason Stryker, who is that?" Guess he went by Jason Wyngarde in the comics...
And who's Jubilee?
Jubilee (in the comics) is a mallrat who can shoot fireworks out of her fingertips. One of the famous scenes with her was playing an arcade game which, subsequently, malfunctions from her unconscious power. Her power level has jumped up quite a bit since those days, but in the comics she's a close friend of Wolvie, much like Rogue is in the movies.
...the camera's swooping over the water, and you see this light thing under the surface. Is that her?
Yes, in a way. If you think back to it, doesn't the light under the water kinda look like a flying bird? Two outspread wings with a body trailing behind? It's meant as a cinematic teaser to everybody who has read the comics - Jean has become the Phoenix, join us in X-3!
What's the Phoenix?
In Greek mythology, a Phoenix is a bird who, every 500 years, dies in fire (of its own creation) only to arise from the ashes more powerful than it was before. You may have heard the phrase, "Like a Phoenix rising from the ashes". The Phoenix was used to symbolize rebirth and resurrection, as well as great power consuming oneself.
In the comics, Phoenix is a God who takes an interest in Jean Grey. Jean sacrifices herself for the other X-men, piloting a space ship down from orbit during a horrible solar flare. The radiation was thought to have killed her, but in actuality the Phoenix stepped in right before Jean died. And, if you remember the movie, something similar happens there as well.
I'm glad that the screenwriters are taking story arcs from the comics and adapting them to the movies, but I'm worried about how they're going to resolve the resurrection of Jean in the next movie - I think that average moviegoer won't accept "Oh, Jean, yeah, she didn't really die, she was resurrected." I mean, it's one thing to accept miracles like that in a comic, it's another to accept it in a movie.