You can research enforced loyalty, and purchase that upgrade to prevent opponents from colonizing that planet, until you are ready (have civic labs, and researched ice or volcano colonization, etc.).

Yeah, they can pass by easily, but not without some damage (30% of hull), and all loss of antimatter.  It helps to have a phase jump inhibitor there too, and or another SB waiting at the next planet with other defenses, like mines or enhanced Vasari turrets that prevent regeneration.  

I agree, that a SB alone, is not enuf to deter them from just jumping past.   I personally would like to see more damage for bypassing the Starbase, including damage to the shields.  Maybe -50% for all, upgradeable for TEC to -67%!  That might be a real deterrent.  Right now, people pretty much ignor/bypass SBs, and like you say, use them more for offense!

Glad a few people notice this.... entrechment, really should be entrenchment!!

first off, the vasari´s orculus SB can move, so this one has a certain offensive potential (when attacking a hostile planet which later, if succesfully occupied, will be yours). this might also be important as the vasari have no "true" anti-SB vessel, as the TEC torpedo cruiser, for example (except for a heavy fleet, of course )

second (i haven´t tried this out yet: but from what you´re saying, allies can also build SB´s in your own grav well):

it seems like a popular strategy to completely avoid the SB´s and jump nonetheless, intentionally accepting the consequences. this is, among other relevant things, accomplished by planning the arrival spot of the phase jump so that the fleet gets away without being hit by ONE starbase.

so, if carefully placed, i could imagine that TWO starbases (one by you, one by your ally) being built near the same phase line can block it completely (meaning no hostile fleet can pass without heavy losses).

and finally:

i personally think SB´s shouldn´t be too much overkill. in case of doubt, they serve a good role of slowing down and hampering the enemy, but that´s it.

no SB, and may it be max fed up with offensive and defensive upgrades, can withstand a pretty fleet for long. and that´s a good thing to know