(I also have not seen a single AI starbase with any of their abilities researched, it's always just passive upgrades). Taking the starbase into account for retreat logic would only work if the fleet stayed with the starbase, otherwise it's false logic if the starbase is nowhere in range to help their fleet.
Agreed and agreed. I too have never seen the abilities used by the AI, which is obviously a dissapointment and oversight. Also, the fleet AI does need to be reformed to take into account the cost of SB's and their tactical value, but it must be done so as to also take into account that the starbase actually needs to be on 'this side' of the gravity well.
Personally, I don't mind the number of starbases built by AI, as I tend to do the same, using the trade upgrades and culture ones (almost always play as advent) for every world, regardless of whether it is front line. Whether the AI is also doing this is questionable though, especially in light of their obviously not making use of the abilities upgrades (who is to say they are getting the economics ones?)
Hopefully these will all be addressed in this coming patch.. which I am very much hoping is coming out in the next couple of hours -- I have a long long train ride perfectly suited to Sins! 