Here is a novel suggestion.
What about upping the dmg mitigation for Capital Ships from 69% which is the max now I believe to 79%? Furthermore:
Give a general 10% or 15% buff to hp and shields to all capital ships in general, this will only somewhat solve the problem. Then add a lv. 4 tech that allows you to start out with lv. 3 capital ships whenever they are produced from the shipyard.
There is already a tech at least for TEC where Cap Ships earn experience faster but its high up in the tec tree and even with that tec leveling up Capital Ships to a useful lv. is hard-tough going when starting from lv. 1.
In addition to a weak Flak for capital ship, which really is mandatory as many have already mentioned (for defying sheer logic) can make cap ships serve a much better role in SINs. As of right now pretty much anything can counter a capital ship and a capital ship doesn't counter anything. Its only made much worse by the fact its the only non-spammable unit in the game.