My Thoughts
With the goal of trying to balance simplicity with fairness, I think this is what is best:
Prices will be updated with a new algo that weighs DT and Damage Output more heavily, and capacity to carry other units less so. Prices will also be dropped slightly overall. On the flip side, a ship/facility will get generic capacities listed (4 SF Squads, 20 GAVs, etc) and come with NO onboard units when built.
That means you are free to put whatever units of whatever size on your ships, if you can afford them.
From past experience, especially as an NR player, the cost of expensive SF and Aux units catches up to you, since they are small and suffer high losses. So eventually the game should balance itself out a bit. Also, with a few exceptions, there aren't MASSIVE differences that aren't also accounted for heavily in cost (TIE F vs B/W prices for example). And for GAVs, theres even less of a concern in my mind. Again, prices for similarly powered units are similar enough that I'm not too worried about abuse here.
More to come soon.