A starbase in the hands of the AI is quite weak unless it is very close to one of their star systems. The reason is that it never puts a single squadron on one, so you can just wipe them out with squadrons yourself without ever risking a ship or squadron. The severity of this can be reduced slightly be giving the starbase units some chance to intercept - I have tested a 20% chance and it doesn't solve the problem, of course, but it does slow the process down and will occasionally cost you a squadron or two before the starbase dies.
I should also point out that I don't think I have ever seen the AI upgrade a starbase. They are always just the regular version, never the delta or omega.
A very good point (or two), but there's an additional problem: the AI only seems to use missiles if they're nukes - and that's not FF specific.
You're also right about the AI not upgrading starbases; I'm not sure if that's simply a matter of calculating whether it's cheaper to rebuild one after destruction. To be true, I've hardly ever seen a starbase get attacked; the main targets seem just to be star systems (which is a bit obvious as that's what counts in the end). Personally I only upgrade starbases if a) I can afford it and b) stronger spaceships appear in the game (whether barbs or regular AI). As far as I can tell, the main AI reason to build a base is to get at resources and to rely on ships for attack/defense of systems.
Perhaps with reduced fighter/bomber ranges the AI will use starbases as intended?