I was thinking that in order to make Starbases a little more useful without overpowering them a good option would be to give the base a option to drop a beacon in any connected gravity well, while this beacon is active any enemy fleet taking the phase lane between the base and it will have there course corrupted and be forced to come out of phase space at the beacon. This would most likely make it more likely for the attacker to deal with the starbase instead of bypassing it in order to avoid jumping into a ambush and would still make it possible for a faster raiding party or larger fleet to pass through the trap.
For the Mines I think it would be better if when you deployed them it created a small station that would produce a ring of mines around itself for however many credits in a similar fashion to a hanger creating ships each station could support multiple rings with a increasing cost per ring. This could also be interesting in that the control centers could have other abilities such as salvaging debris in order to lower the cost of mines or replenish them. This could also simplify mine clearing by allowing a the various defense busters in addition to a scout to destroy the center disabling the field.
For the Advent super weapon I would also like to see it to cause all enemy ships in the targeted gravity well hallucinate and attack each other for a short period as well.
I would also like to see the Advents Radiance Battleship’s cleansing brilliance ability have its damage lowered and become a area attack firing the beam from multiple spots on the hull in a kind of sphere like lazery ball of doom. 
One final thing I would really like to see is some kind of flag or mothership a massive wicked looking ships that would when finally researched and built would take the place of the capital planet giving it’s bonus to whichever of your planets gravity well it is in. These ships could also carry a large population providing some additional income, they could also be upgraded with a number of offensive and support abilities as well as some economic modules. They would have to be very deep into the tech trees possibly a final research spot in all three trees and would cost a huge amount of resources and require multiple capital ship crews. A disadvantage could also be added to them in that if destroyed a percentage of your planets would freak out and revolt turning neutral.
So far I have really enjoyed entrenchment although I would have liked to see some more planets, relics as well as more ships, structures and technology added. For the cost though I defiantly think it’s a decent deal with what it does add.