Allow members to upgrade base modules similar to how they upgrade the base. Each module would have 3-4 upgrades depending on what it is/does.
Lets say you have a null turret. It takes up 2 spots and adds 1600 attack.
Upgrade 1
targeting sensors: adds ability targeting sensors which can randomly activate when the base is attacked boosting this turrets damage output by 400 (2000 total attack)
100 Tachyon Cylinder, 25 continuum beacon, 35 subspace seeker, 1000 energy
Upgrade 2
exotic matter pulse: Adds a pulse of exotic matter raising the attack 15% (1840 total attack, 2300 total with targeting sensors activated)
25 crimson obelisk 20,000 exotic matter, 1000 energy
Upgrade 3
sub system analyzer: adds ability raising critical hit chance of the base when defending 5% which randomly activates when under attack
200 weapon probes, 200 defense probes, 250 complex tech parts

These would boost individual modules or have affects that stack. In this example upgrades 1 and 2 focus solely on the one turret where as upgrade 3 affects the entire base. However if multiple weapons modules had that upgrade the affect would stack from 5% for one, to 10% for two and 15% for three and so on.

These upgrades could be applied for all modules.
More creative upgrades could use things created from the creative theory lab or even mission based rewards.

+1