I wrote in a previous discussion that, in my opinion, FFG should release Republic ships for the Empire (Venator and Acclimator) and modified/salvaged CIS ships (Lucrehulk, Providence, and Recursant) for the Rebellion.
From here a Clone Wars campaign box can be released with new Republic/CIS cardboard for each ship. (The campaign could come with a fighter pack to add Clone Wars era craft to the mix as well.) Campaign restrictions would limit which vessels can be used by either side, creating a Clone Wars setting for Armada without adversely affecting existing game balance.