Unlike the other thread, this thread isn't about ******* but rather contemplating if and how best to have clone wars ships.
I see three possible ways to have clone wars era ships.
1. Introduce 2 new factions to armada, the CIS and the Republic.
2. Add the ships to the existing factions.
3. Make a separate game.
I think the second or third option make the most sense in terms of balance. Trying to hamfist 2 new unique factions this late into the game is folly. There's only so much variety available with 4 hull zones, 3 dice, and 3 ship sizes. To try and make a 3rd and 4th faction with their own unique play styles would result in them being either overpowered, underwhelming, or just plain gimmicky.