The story seems pretty interesting. There are some good things, but there are a bunch of things I feel could have been improved.
First the good stuff: It is nice to see the how the Jedi and the Republic are starting to falter. Also, Maul has proven to be a good villain, but I'm not sure if Dooku was needed. I think Gunray would work better as the face of the Separatists since audiences can recognize him more.
We see more of Anakin's fall to the Dark Side as he becomes more aggressive and I'm interested to see how it plays out in the Clone Wars. We also get to see him work with Obi-Wan in an interesting scene with the undercover Jedi. As for Obi-Wan, he's a lot better because he gives actual lessons to Anakin while more compassionate and understanding. He cares but he's not going to put up with any nonsense.
The rest: The final battle is basically the same as in AotC: a bunch of jedi come in, and then the clones come in to the save them, leading to the battle. I think it'd be easier if you just have the Jedi and clones come in at once.
Also, Padme's role has been decreased a little, in my opinion. In the last film, she was Anakin's love interest, but she also played a huge role with the invasion.Here, the only thing going on is just her marriage and affair with Anakin. I like it, but maybe she should have had a significant role.
Finally, add in some conversation with Palpatine and Anakin. Show Palpatine putting some doubt into Anakin about the Jedi, or maybe at the end (when Anakin's recovering), Palaptine's there to "comfort" the young Jedi and begins to put the seeds of the Dark Side.
Nitpicks: I do like the romance between Anakin and Padme and I do understand why you made it this way, but it felt weird that Anakin and Padme didn't get married, to me anyway. Maybe it's because I'm too used to the actual PT and other PT rewrites I've seen where they do get married (This is more of nitpick, really, not actual criticism).
Overall, I think the story is good. The criticisms I just stated are small in comparison to the rest of what you wrote. Keep it up. Can't wait for Episode 3!