Okay, so something I have noticed on the forums is that capital ships are a divisive issue. Some people find it preposterous that you can crank out Kol battleships at two research stations, but need a buttload to put out the Kodiak cruiser.

So, a proposal:

Give each race a seperate "Capital Ships" research panel. This panel will be divided between the types of capital ships available. Now, you won't have to research the ships themselves - everyone knows how to make a big friggin' ship! It's just a big ship!

What you're researching is unique subsystem upgrades that are neither active nor passive leveled abilities. For example...

The Kol's ion cannon beams would be a good example. Before you research this, those spots are simply regular laser turrets. Research the ion beams, and they become the ion prongs of doom we know and love to watch dig into our enemies.

Another example would be the carrier subcapacity of each warship. Every time you research this, to a maximum determined by the type of ship, you can build and maintain a new squadron from that ship.

And so forth and so on. When they start out, a capital ship will be a big platform for lots of little guns, planetary bombardment, and maybe a couple of fighter squadrons if it's a Sova.

At the endgame, they should be powerful juggernoughts mounting multile BFG turrets and converging multiple beams of death upon the enemy, sending flight after flight of raptors and falcons screaming out of their bays to bring the rain down on the enemy.