The only issue with starbases starting with capital ship level weaponry is that you would then have to require a player to *pay* for all that weaponry. There are cases where you may want a starbase somewhere for reasons other than combat. For example, the listening post I mentioned, or maybe just a cheap phase inhibitor deployment to slow ships down in an otherwise uncolonizable system, or to beef up your economy or culture with installations in uncolonizable systems.
Sure, a starbase should be able to fend off attackers (and I know the whole point of the entrenchment expansion is to add heavy defenses), but I'd rather leave that to an upgrade than to make it required, standard equipment. If you want this particular base to be a defense platform, just add the weapons. Ideally, the total build time and cost would be the same as if it came standard with the stuff anyway.
For a unit as powerful as a starbase could be, perhaps a maintenance cost needs to be assessed to keep people from ... well... entrenching every single system. I know sins has some of this already, but I haven't played enough games where starbases played a major role to say I've noticed whether they noticeably impact my economy.