I am sure these have all been mentioned but from multiplayer against multiplayer this is what We have come across.

*when upgrading star bases especially armor "from 3000 to 6000 hit point"  it only upgrades to 3750 and never more even     with multiple armor upgrades.

** Late in the game when doing research it generally will send your cash flow in to negative 

*** Mines rarely work for TEC and Advent, Vassari seems to work ok

**** clarity on what ships will be mine sweepers "the scout is for TEC, but others are unknown"

***** When building multiple of one type of unit you seem to get a refund on some of your funds "usually cash"

Some upgrades I would like to see:

* when upgrading weapons it is 5% "this is less then 1 point of damage added onto ships with bases in the 10-19 range"

** fewer mines that work better.  Late in a long game I am barely able to find my units beneath the clutter of a gravity well chocked full of mines edge to edge.

*** But most of all let the starbases Move around in the gravity well "I know Vassari does"  If you spend all the money on them they should be capable of defending the planet not just the small ring of destruction where you place it. nothing is more aggravating then dumping 10 grand in a base and the enemy sidesteps it and attacks the backside of the planet.