I'm all for trying to take the cartoonish aspects out of the PT and ROTJ but like the Ewoks in ROTJ removing the Gungans (I'm still very very open to any ideas how that could be done and leave a feature length movie behind) from TPM possibly creates more problems than it solves.
Which is why I have concentrated more on making the Ewoks and the Gungans into believable alien people, instead of spawning comedy enemy troop erasers.
If we had more footage of the people of Naboo fighting the invaders and a more clear goal for the Feds invading the planet it might be possible to drop the droid vs Gungan battle making their presence en masse totally redundant.
That would be an enormous undertaking but not beyond the realms of a fandom that can assemble huge numbers of grown men and women in full costume every few months as soon as a convention or major fanfilm shoot is announced.
My take on why the Emperor used the Trade Federation, Banking Guild, Commerce Clan, Credit Cardland, Saving Stamp Squadron etc as the other end of his take over was they too would be a threat because of their accumulated wealth. It's very dangerous when the political arm of a society and the forces of commerce lock horns, they are just as good at eating each other as they are in feeding each other.
If he barged in a declared himself dictator they would have the resources to have him removed (he may be a Sith but he couldn't take on the whole galaxy and once).
By getting one side to fight the other he wipes out both the Jedi and the wealthy commercial end of the Old Republic.
He also creates an arms race which generates the troops and weapons he will need to stay in power once the dust has settled.
He doesn't need to fight the Republic, he manipulates it to tear itself apart and build the infrastructure of the Empire in the process.
This was the one really good idea of PT.
The mistake was to make one side comedy villains and the other side a creepy cult with very little in the way of brains.
If both sides represented aspects of what was great about the early days of the Republic but turned against each other it would have been more tragic, more epic and more in line with tone of the OT.