Though I haven't got the Entrenchment beta, the feedback seems to imply that the starbases are too easy to bypass.

How about the sirens concept, as a special power?  If one type of the starbases was able to entrance a selected ship from a fleet to approach more closely, that would block a grav well effectively?  That only leaves the other type to have extended range, perhaps with missiles. 

Another concept I wondered about was a phase 'wind'- why have travel along all phase lanes the same speed, when it could be faster or slower, and dependent on direction?  The pirate base could be harder to approach.

Lastly, Charybdis and Scylla- how about a phase creature that attacks ships?  It could gain another head for each ship it kills, and have an asteroid lair, where it can be finally destroyed- only being dissipated otherwise.  It might be attracted by multiple ship signatures of the same type, a sort of space smell....