EddieDean said:
4) The structure of the ending. It has to deliver the lowest lows followed by the highest highs, which is mainly an issue of ordering. (And personally I’d treat the Gungans as the least important plot there, so maybe cutting that down would be my second major trim.)

I personally like l8wrtr’s approach to the ending, although I think a few things needed better timing (Such as the way Padme’s failure is handled, which I feel should’ve been moved closer to the finish). Naturally, I tweaked it for v3 of my edit and divided it into its own three-act structure, complete with a lowest point followed by a highest point. Here’s my arrangement for those who want the rundown:

Setup
Gungan army intro
Palace siege intro
Space battle intro
Gungan battle begins
Darth Maul intro
Destroyer droid obstacle
Lightsaber battle begins
Anakin enters the ship

Conflict part I
Gungan battle continues
Lightsaber fight continues
“We don’t have time for this, captain.”
Anakin enters the battle
Jedi get separated

Conflict part II
Gungans retreat
Padme gets captured
Qui-Gon dies
Gungans surrender
Anakin gets hit
Obi-Wan fights Darth Maul
Padme meets Nute Gunray (With Padme’s comeback deleted)

Ending
Darth Maul dies
Anakin destroys the control ship
Gungans celebrate