It seems only natural that once the basic rules and ships are established for the game (consisting of a generic time frame of the original Star Trek series, but much more fleshed out with obvious changes), that the groundwork will be layed for taking the rules and going back to the Enterprise era and forward to TNG area.  Since Starmada allows you to "build" ships, this would be theoretically possible..much more than FC since building ships is not part of the game system.  This fact should make this game even more sweeter.  I know you would have to come up with new rules and modifications to the system, but it could be done..something not possible with the other game systems.  I know this would have to be player done..but it woud be fun.
I was just thinking about how Enterprise era ships used "polarized hull plating," which could be used as an advanced armor plating in Starmada.  All the other stats would just be scaled back.  If all ships were scaled back equally, you could get the feel of an earlier era.  That's the beauty of Starmada..if you can dream it, you can build it.