Hay Ronin,
First off love the art work, best of luck on that.
Hay I wanted to run a tech tree idea by yeah. Ithought I might use it in my mod as well, but I think it could work for your mod as well. OK, bare with me its in the rough draft stages:
All the ships sizes are avaiable from the start, ie Huge, through tiny. To balance it out the capacity of ships is really low, such that the tiny hulls can not carry engines, which is good and represents the fact that fighters can not travel without carriers until the fighter warp/hyperdrive engines are developed.
Instead you, develop ship role techs, such as carriers, destroyers, cruisers, battleships, command cruisers. These serve as commonents that you attach to your ships just like some of the new components in TA, like the warp bubble could be used to create a "carrier" maybe tweak it a bit. The others I am still working on, maybe destroyer adds weapons and ship speed at the same time, its really a matter of examining the various roles of each ships class, IE Destroyer, Cruiser, Battleships, Frigate and so on and trying to translate that to the game. I think it might be cool because it would allow people to really develop a fleet in their own fightinng style, big and powerful or quick and manuverable, you could also assign a style to each faction spo the Federation builds well rounded ships, the Klingons build slow powerful ships and so on.