As its been said, lots of people hate the prequels, but i don't know anybody that hates them because of the ships, Darth Mauls ship would look awesome on the table, the shiny Naboo ships would look great too!
you don't have to limit it to republic (composing Nabooo ships, Jedi fighters and clone ships) Vs Separatist ships, which wasn't purely droid ships. also, you don't have to think about a thematic reason to have imperials fighting republic - I've had my rebel squad fly against a rebel squad - it happens!
you don't have to limit it to just those two factions, there's plenty of other ones in the EU, you could go back to the knights of the old republic era and have Old Republic and Mandalorian factions, Jedi Order and Sith Empire. i think so long as each faction has a unique and interesting theme that's more important. you could have very old fighters that have much weaker stats that the modern ships, but the Jedi or Sith flying them have access to powerful force abilities to even things up.
if the new factions have their own upgrade types it would limit the number of existing ships a new player has to buy to 'catch up'
I've only been playing a few months but i still have a long list of ships and upgrades i need to buy. don't get me wrong, i'm not buying ships i don't want. i don't care how bad i want c-3po i am NOT buying the tantive for that alone!
that's where i think that expansions like the aces and most wanted are a good idea, if they had more expansions that consisted of about 2 preexisting ships (with repaints naturally) but new pilots for them and other ships and a mixture of brand new upgrade cards plus a few upgrade cards that either only exists with other factions ships or the big epic ships then i think an expansion like that would actually exite me more than just another new ship.