1) Removal of Anakin as Vader: This I don't like, simply because for me, the Star Wars Saga is IV-V-VI-I-II-III (and then a reprise of IV-V-VI, actually), but it does look like you'll be able to pull this off as well as it can be.
2) Trimming the opening battle: Yes! Just make sure you remove those pesky Buzz Droids...
3) Unused score: I'm not really sure on this one... More Williams is always good, and I like what I've seen in what you've uploaded, but it might be too much of a good thing... Difficult to say without seeing a complete edit.
4) Deleted scenes: Again, I'm not sure. I was never too fond of the Rebellion subplot, I think it at the very least needs some trimming before being included. I definately suggest you use the "Plot to Destroy the Jedi" deleted scene, as I find this single scene to make Anakin's turn a lot more believable.
5) End battle: This is really good. 'Nuff said.
6) Qui-gon conversation: A really good idea, but hard to pull off. I like your visuals, but the audio just doesn't sit right with me.
7) Removal of Leia: See #1...
As for the Dooku fight, it's just awesome! Although Dooku's execution doesn't really feel like a "spur of the moment" thing (which I think you intended it to be?), I really like how Anakin coolly and deliberately (as it seems to me) snuffs the Count. Palpatine's dialogue afterwards is also perfect, in my opinion.
I'll be looking forward to seeing the finished product, and I have high hopes that it will be a worthy replacement to the travesty that was the official version. Best of luck on your project, GM!