Just a couple of ideas how to improve the game and open up new strategies.
Advanced Warp Sensor
Give Advanced Warp Sensors 2 new abilities that would hack/mess (not an actual HACK. would NOT cost HaP) with the AIs warp in stuff thingies.
The first one would delay the wave by a couple of minutes (2 or 3?) and the other one would make the wave spawn instantly.
The player could activate these abilities by adding them to the "build queue" and "building" them. It would cost some resources and put the Sensor on a cooldown. Max 1 Advanced Warp Sensor per planet. Knowledge cost for unlocking would be increased to 1250.
Zenith SpaceTime Manipulator
Make them give 50% of the speed buff to adjacent planets.
Harvester Exo-Shield
Change name to Exo-Shielding. In addition to shielding Harvesters it would also double the health of Engineers, Rebuilders, Cleanup Drones, Scout Drones, Mobile Builders, Colony Ships, Energy Collectors, Matter Converters, all constructors (no warp gates) and Command Stations.
Counter-Dark-Matter Turret
Change name to Energy Shield Generator and change it's category from "Turrets" to "Support Ships" (Or just add a new "thing"?)
Reduces the damage taken from Energy weapons by 20% (Energy Bomb, Energy Wave and Energy Burst). Costs 3000 Knowledge.
Economical Command Station
Mark I: Increase energy production to 25000 and resource production to 45/45
Mark II: Increase energy production to 50000 and resource production to 90/90
Mark III: Increase energy production to 75000 and resource production to 180/180
Logistical Command Station
Mark I: Max enemy ships speed 64 (planetary) and resource production to 28/28 (average of economical and military). Also repairs all nearby allies (5000 range)
Mark II: Max enemy ships speed 48 (planetary) and resource production to 64/64 (average of economical and military). Also repairs all nearby allies (10000 range)
Mark III: Max enemy ships speed 32 (planetary) and resource production to 128/128 (average of economical and military). Also repairs all nearby allies (15000 range)
Military Command Station
Make the Railgun disable Warheads.
EDIT:
Armored Ship Hangar
Holds up to 200 ships. Repairs the ships inside and protects them from Nuclear explosions and EMPs. 10 million health and 100000 armor.
Terraformer
Terraforms the planet (or whatever) to provide supply even if it has been destroyed. Can be built anywhere with a Mobile Builder.