A few thoughts on capitals

I like the fact you get a flagship when you start, I'd argue almost essential for clearing planets to colonise early on and great for crippling a nearby enemy if you can take out his capital without losing your own if its a crowded map.

Now I also agree that capitals should always be open for building from the start it creates alot of tactical options and adds much of the early/mid game flavour. if they were limited everyone would be forced to turle early/mid game.

At the same time it would be nice to have some endgame units that would perhaps compliment frigates and crusiers.

So I suggest Supercapitals , require 3-5 capital crews (cost 3-5x capital maybe more) , very tough but only marginally better firepower certainly not a solopwnmobile. but they would have some sweet special abilties that would make frigates and/or cruisers alot more effective in combat.
E.g. Antimatter feeder, or repair station regens rates, Coordinated firing (the more ships in the link the higher the damage bonus) etc etc

Put them round 7-9 military labs and perhaps the better special abilties to 15.

Theier weakness is that they are a single ship and thus are a major Target for enemy fleets who might suicide a couple of capitals to ensure they kill your supercaptial making killing the support fleet much easier