Some of my ideas (which I'm sure have been posted a thousand times):
I believe that the fighters for all of the Prequel Films (Naboo fighters of course) should look different.
The Trade Federation Fighters should be blatant predecessors of the TIE Fighters in both design and sound. Something that could justify the Empire switching to real Pilots compared to a computer is that the TFF crashed with high frequency/didn't have good aim.
The X-Wing Fighters should be the main ones for the Republic, and should be seen in the Battle of Geonosis and Coruscant. They should fly smoother than they do in the OT as they're newer and aren't as damaged as they are later on.
Jedi should have their own definitive type of space craft. In my personal opinion the fighters they used in Revenge of the Sith would work just fine for both Attack of the Clones and Revenge of the Sith. It seems either of the ones shown in film would work though.
Actually, I have to say I would change all of the space ships in the Prequel Trilogy to some degree.
For one, I believe that the Trade Federation Space Stations should both look more ominous and be more prominent throughout the films. I want all of the films to have more of a feeling of consistency and that would add quite a bit in my opinion. However, I feel that there should only be one big space station throughout The Phantom Menace. That's the first time the Trade Federation is involved in any kind of war, and they wouldn't exactly how to handle it yet. As time goes on, this Space Station model becomes more Prominent with each film. In Attack of the Clones, the Separatists are preparing for a full scale war so they would be stock piling on these. In Revenge of the Sith, I would make them the one of the only two Separatist space ships in the entire beginning battle. Not only because it makes them more prominent in the battle, but so we actually have an idea of how big the battle is and what ship is on what side.
The other Separatist ship in the battle would be Grevious's flagship during the Battle of Coruscant, where Palpatine is being kept. I feel that the PT should have it's own Executor which is just as ominous as the actual one from the OT. This could be a ship that Darth Sidious is using, one that appears in every PT battle and is only used when needed. For example, in an extremely edited version, this could be used to rescue to transport Darth Maul to Naboo, evacuate the Separatist leaders on Geonosis, and then be the main space ship in the Battle of Coruscant.
Finally, I feel that the gigantic ships used by the Republic in Attack of the Clones and Revenge of the Sith should be an amalgamation of the ones used in Revenge of the Sith, and the Star Destroyers of the OT. The basic design of the Revenge of the Sith should still be intact, but the deflector shields could be of the OT Star Destroyers.
I have a lot more to add, but it's 1:06 and I'm tired.