MTHaslett: I'm right there with you, I found the Gungan battle to be one of the great action plots of TPM. And like you said, making it a sad defeat for the gungans as the battle goes along can be acheived easily. First we could obviously replace the music with something that sounds a little more "hopeless" or "sad" as they are retreating , maybe some close up shots of the gungans hand to hand fighting. I even thought of the idea of making the scene darker as if they were dark looming clouds on the hills. However, you would have to change every exterior naboo scene to be dark and cloudy (which would be a good step towards a serious visual). Ok, that might be a stretch. Anyhow, I think the gungan battle is just as good of a subplot as the Han/rebel troops attacking the shield generator in ROTJ. And we all would like to be concentrating more on Luke/vader/emp , but it just felt more fun with the cuts between the two.

The underwater sequences: Again I really don't see what information is gained from any scenes the moment they dive underwater to the moment they come out on the other side. They dive to meet the gungans, get no help at all from the boss nass, decide to have a talk about keeping jar jar, qui gon takes jar jar, obi wan looks annoyed, they go through not one, not two, but THREE encounters with fish monsters of various sizes. And all the same time you have to make some sort of a decent conversation with obi wan and jar jar about why he was banished. Then we finally get to the surface, and in some edits we have a waterfall sequence.

That, to me, is just a waisted half hour of a star wars movie. It's like a comic book one-shot story. Qui and Obi's journey into the naboo sea! It just doesn't need to be there and i'll tell you why:
We can establish who jar jar is and what he is doing with his conversation with qui and obi when he runs into them in the forest. While he is chasing qui gon he could say

cut out "are you brainless"
Jar Jar: Are you a warrior? Are you on a journey? Let me come with you.
Qui Gon: you almost got (cut "us") killed.
Jar Jar: I know I need a little practice, but you could use my help...
Qui Gon : that won't be necessary
Jar Jar: Look, i'll do whatever you say .....
Qui Gon: GET DOWN!
jar jar jumps to the ground
quigon takes out the staps
jar jar getting up
Jar Jar: like I said i'll do whatever you say
Obi Wan: whats this?
Qui Gon : a local, now lets get out of here before more of those droids arrive.

Jar Jar: Hey! what are these droids here for anyway?
jar jar runs to catch up
Jar Jar: Look if there is going to be a fight, we need to go to the naboo city...
The two stop and look at each other
Qui-Gon: a city?
(close up of qui gon) Can you take us there?

then cut to the next scene

I know this may sound ebrupt, but if you cut to the assault on the naboo city it sure would be things in perspective as far as the time line goes.......I mean the Jedi spend ALOT of time lurking around in the water, and I don't see why the trade federation landed so damn far away. They jammed their frequencies anyway, this would make it appear that they landed on the outskirts, the jedi followed jar jar to the back door of the city, and the neimoidians are invading the city, then by the time the jedi appear the queen and her entrouge are being escorted to their selected executions. Wa-bam, that's a nice flow to me. The underwanter sequences are just pointless. We can be introduced to Boss and and whatever problems the gungans have in the meeting at the swamp before the battle. I'm gonig to take a gander and re-doing that scene in written form here soon. Comments?