There's definitely some great material here. The idea of moving the brunt of the Gungan battle to the beginning, and thus, being the droid invasion, is definitely cool. There's a lot more to be said, but there are some great ideas here.
However, I think you should be wary of getting too serious in tone. Sure, it shouldn't have poop jokes and "Yippee!" and all of that, but remember, the original thing of Star Wars was a throwback to the fun adventure serials of Lucas's youth. My biggest issue is ending on the funeral scene. If you do that, then there won't be one truly upbeat ending in the whole prequel trilogy. Also, musically the transition to the end credits would be really rough. Even ROTS ended on the hope of the Force Theme to give it some life and a workable transition to the end credits (something I had been concerned about before the film released). I'm definitely in agreement with darthpreston's words a few pages back: the obvious conflict is resolved by the end of the film, and with the Gungans freed, there is certainly cause for celebration. I suppose I could rant about this, but I guess you see what I'm saying.
And overall, I wouldn't ditch some of the adventure elements (underwater chase, for instance). I think it would work in your favor to try to tweak some of the side stuff so it's more effective, as opposed to ditching it, if you see what I'm saying.
Another thing to consider is that TPM very much mirrors ANH in its having one character lead to another. We first meet Qui-Gon and Obi-Wan, who get threatened by the Neimoidians. From there we meet Jar Jar and go to rescue the Queen. Now the group goes to Tatooine and meets Anakin. In ANH, we first meet the droids, on a ship that gets attacked by Vader, who takes the princess, who sends R2 with information for the Death Star. The droids escape to Tatooine, where they meet Luke, with whom they find Obi-Wan, who takes them to Mos Eisley to meet Han and Chewie. So there are merits to taking a little time and enjoying the ride. You don't have to rush to Anakin necessarily. Should he be the focus? Sure, but we don't have to find that out right away.
Please don't take this harshly; there are really great ideas here. And if I'd followed the thread from the start, I could've addressed issues as they came along. I'm just concerned that in focusing on the story and the thrust of the film too much, we can run the risk of not enjoying the ride as much as we could. I hope this makes sense. Keep up the good work!