If you see this, bypass it.  I've been on the giving and receiving end of a Vasari starbase in a plasma storm (in a few cases this was a choke point that couldn't be avoided!).  This is not the kind of thing you want to take on without decisive force.  Fortunately there won't be repair bays so it is possible to take it down by brute force, but be prepared for one hell of a fight.

I only buy two weapons upgrades.  I personally find the third one wasteful.  I also find that two hull upgrades are usually sufficient, though sometimes you need three.  Whether you get deflector shield and debris vortex is really based on what you expect from a starbase.  In general, debris vortex isn't worth the price against players, simply because anyone worth his salt isn't going to suicide enough units to create sufficient debris for you to use this.  That said, sometimes players will try to brute force your starbase, and debris vortex can be the ultimate way to punish this.  A combination of debris vortex and deflector shield can be really nasty.

Don't use colony pods, they suck.  Trade is worth your time, especially to extend your longest trade route (sometimes I build a starbase just for this purpose).  Phase stabilizer and enforced loyalty are useful, but situational.  Get them if you need them.

I reiterate: if you see a heavily upgraded Orkulus in a plasma storm, bypass it.  I'd take my antimatter/hull loss from the starbase if I had to, but I wouldn't dare try to tackle such a powerful Orkulus in a plasma storm.  I might attempt it with a massive fleet (1000 command, not counting any [useless, obviously] bombers), but certainly not if it had backup.

Shhhhhhhhhhh........ don't speak about it! I don't want to see my beloved Vasari Capships nerfed for suddenly being viable!