I'm not even sure where to begin!
Alot of great thoughts to think about!

But I think I'll start with the gungans.
This MUST be figured out before anything else...*I* think.
So, first, IF we use the briefing scene, take a look at the background...gungans! So we can't kill them ALL off.
Second, I really like the idea of concentration camps, but it looks as if there is only one shot in the movie that really shows this idea (the one with the droids leading the gungans with their hands up).
AND it seems like there won't be a good way of roto-ing anyone out of those frames.
So, with that in mind, chew on this idea:
Sometime, before the all the fight scenes at the end, we establish that the gungans are being enslaved (like Erikstormtrooper suggested) and are going to be loaded onto the TF ship.
That's why the gungans are in the big clearing. Some ship is going to land there and the gungans will be loaded onto it (the shot of the gungans with their hands in the air).
Jedi fight, Anakin flies, Queen does her thang, and Jar Jar (with a few other gungans-...maybe tarples?) go to try and free as many gungans as they can at the concentration camps.
Now, obviously, you would have to manipulate some of the shots to make this work...like roto Jar Jar out of some earlier scenes so he could actually achieve this goal...hmm.
I'll put some more thought into this...
Oh, and another thought on that: Jar Jar could be more heroic in this scene by having him release those blue ball things onto the droids...?
Thoughts please!
