Flavor is important - if a Venator is better than a VSD or ISD, why would you use (or even build) the newer ships? I believe it would break the mood somewhat. So the GAR and CIS ships are statted as state-of-the-art ships fresh off the dockyards, while their Rebel and Imperial counterparts are presented as either refitted and modernised models (which will retain much of their overall power but vary in configuration) or as weaker, obsolescent units with underwhelming power for their size class.
I might do Rebel versions of the Munificent, but probably not the Venator. I don't want to gray out the fleets by giving them all access to the same ships; it would dilute their character and make the game less interesting overall. Cross-faction Dreadnaughts and Nebulons are probably enough, and I'm not even sure about the latter one.
Of course, for a campaign or special scenario, anything goes. At the moment I'm playing the Heroes of the Aturi Cluster campaign for X-Wing and I think it's magnificent . So much so that I'm toying with the idea of developing something similar for Armada. The only thing holding me back is the fact there's so much still left to do on Shipyards...