Upgrading ship modules:

The idea here is to extend the use or ability of modules you have making scanning more important in battles and making scrapping or swapping modules an idea to consider due to the affects that could be gained or lost by switching modules.

This works by linking with current systems for little or no deck increase in size. They boost these modules often by % or add new affects to them.

For instance, a relay conduit optimizer which increases your charge by +1
or in the same field reinforced conduit housing that decreases energy loss due to the relay by 3%
Both of these would be rare drops and require the player to have say 5-50 complex tech parts to install it on their ship (maybe even higher depending on what it applies). Some super rare drops could have multiple effects or just large effects.
Each module can only have 1 attached (so both bonuses of +1 charge and energy loss -3% could not be had at the same time on the same relays) and stay with that module until it is sold. (they get repaired with the module for an added cost of course).

These upgrades would be acquired one of three ways.
npc drops, techs on the regular tech paths, and a system similar to the creative theory labs.

Add these upgrades as they make sense to random drops from NPC's. Occasionally add them to random bits on the tech tree as well.

As for the third option this would be located in your research tab. It would read as module improvement research. When you click on this rather then having a completion meter like there is now it would simply hold all the research you put into it. Once you reach a minimum level of research (lets say 1000) you would be given a *discover* button.
At this point it functions like receiving artifacts. When discovering each tech has a research cost applied and a % chance to randomly discover said tech. In addition however there would be a rather large % chance to find nothing with just a loss of research points.
Something along the lines of:
25% chance to lose 5% of stored research points
10% chance to lose 10% of stored research points
10% chance to lose 20% of stored research points
10% chance to lose 40% of stored research points
10% chance to lose 50% of stored research points
5% chance to lose 75% of stored research points
(please note these stored research points are the ones put into the research department, not the ones you gain every hour)

The remaining 30% of the time you would discover some tech based on research points invested. If you already discovered the technology it will simply result in the loss of research points equal to that of the already discovered module upgrade.

More ideas:
Shield Energy Dissipater: +5% damage to shields
Hull Crippler: +5% damage to hull
Force Field Life Support: +5 Shield Charge - Only added on shield modules
Electron Compacter: +10% energy - Only added onto Reactors
Universal disruption scanner: applied to weapons modules
This scanner observes all disruptions caused by fired weaponry, gives 5% of weapon damage as research. (doesnt lower damage).
As you can see their effects can hit on almost any area of the game.
Debris collection droids: applied to hulls
Some debris move slow enough to ignore our shields and embed themselves on the hull, these droids clean them up and analyze them. Boosts artifact production by 5% of the hulls value. (ie 400 hull module would give 20 artifact production per hour)

These module upgrades are discoverable on enemy ships in a similar fashion to the way a player sees modules currently.

Upgrading Base Modules:

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. They would be upgraded similarly to how the base as a whole is currently upgraded.
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 any module.
More creative upgrades could use things created from the creative theory lab or even mission based rewards.