Yeah, I sort of thought that, too (about Ani vs. Dooku) but they never expressly say that. He only says 'My powers have doubled since the last time we met, Count.' Actually , if you read the book Labyrinth of Evil which directly leads into Episode 3, they have another 'three-way' shortly before the movie. They made it so that you can think one way if you only watch the movies, and you'll be perfectly fine that way. But those who follow the expanded universe will know otherwise.
It's sort of like what Bungie does with Halo--they essentially have a completely changed storyline if you read the books, but they still make sense with the context of the games.
If we follow the games, the Chief is the last of his kind, period, and has been for a long time. However, if you read the books, he interacted with other Spartans hours before the first game, and they are all PRESUMED dead, which isn't the case at all. Then, at the end of the fourth book, which takes place right as Halo 2 is ending/3 is beginning (SPOILERS AHEAD SPOILERS AHEAD SPOILERS AHEAD) we know that there are, in fact, still other living spartans but they are stuck in Slipspace, on the 'shield' planet known as Onyx. This is the presumed planet that Master Chief is seen floating towards in the secret ending. Thus, the Chief is the only remaining spartan that is fit for active duty (END SPOILER END SPOILER END SPOILER)
Either set of gamers/moviegoers (those who only watch/play the core series, or those who follow the expanded universes) can have their version of the full story.
As for the first half of your post, the game is based on the entire series, not just the movie, which is being used as a gigantic pilot episode.
Could I trouble you for some maple syrup to go with the plate of roffles you just served up?
Tag, courtesy of fkusumot: "Why do most of the PS3 fanboys have avatars that looks totally pissed?"
"Ok, girl's trapped in the elevator, and the power's off. I swear, if a zombie comes around the next corner..."