My games tend to be long too, but i usually only get to play about an hour a day, so my games last for about a week on average, sometimes two weeks if im in a larger map, or if things get more complicated than i thought in smaller ones.
As for Starbases, i dont know what to say, i have lost SB's too, not that i cared for that too much, and i thought of tweaking the buffs for the hull and shields to make it stronger, but haven't done that yet. Though, if i lose them consistently i might do that, just to even it out a bit. But i have to be careful of that, so i dont make it too strong, a ship that can take everything isnt any fun, haha, but i suppose you could make it take a whole large fleet to take it down. And perhaps extend the range and tweak the damage down so it doesnt kill "Everything" that comes across it. Maybe just most. And as too fighters/bombers? Hmmmm... that is a sticky one, alot of ppl like that strategy and the strikecraft can in fact take out a lot, and they replace fairly quickly and usually at no cost for the carriers and caps that have them.
Only thing i can think of course would be to give the SB's and maybe the Capitals as well, anti-fighter guns, so that even spammed their easier to counter. Extra hull points and or shields on the caps might make them less susceptible as well. Which would mean the strikecraft spammers would have to try something else. As for Single Player games, it might be interesting to see how the AI counters. I haven't tried anything like this yet, so i have no idea. Sometimes, things like this work and make it interesting, sometimes, they botch up the balance and i wind up going back to normal.