how about this: when construting a starbase, the vasari get to chose between the standard starbase as we have now and the assault starbase which swaps basic and second tier weapons slots. as such, the assault starbase becomes just one big, bad, upgradeable structure buster, but it comes with this function right out of stock. only, that also means it won't be as effective against ships than the standard starbase would be.
I think this takes care of several problems: 1) the vasari still have a unique way of dealing with enemy structures. 2) it makes it a bit easier and faster for them to get to this point. 3) it does not necessarily make it stronger, since it will still be vulnerable to ships. 4) the enemy will have some time to prepare. even without the requirement of an extra upgrade, the starbase will still take a while to build and will still only have the stock 3000/2000 hp.
maybe it's a crazy idea or even stupid, but beta is all about suggesions. I dunno from a coding point of view, but just copying the stock base and switching the ports ... well it should be doable with reasonable effort I hope.