Some suggestions, though these have come up before. And I think these will be a pain to implement, so just keep this as a suggestion.

Sabotage
A new action that is available when the NPC has triggered an ability that increases it's attack/defense.
Costs: 25 Energy
Action can be performed only once (per ship if elite/boss) until the triggered ability wears off. If one player successfully sabotages, no one else can perform the action again until the current ability wears off.
Chances: Maybe 35% Success / 65% Failure.

Examples:
Renegar, Lazuli Station
Ability: Lazuli Fighters - Will sometimes launch attack fighters, boosting its attack by 25% for 1 hour. (Maybe 3-5 fighters total)
Sabotage:
If successful: Sabotage the fighters, making them weaker. Triggered Ability attack boost reduced by 10%.
If unsuccessful: All fighters lock on your ship, you take heavy damage. (Damage based on total hull)

Dark MegaComplex:
Ability: Phase Overcharge - Will sometimes overcharge its phase pylons boosting its defense output by 25%. (Looks like 3 pylons)
Sabotage:
If Successful: Sabotage one/two of the 3 pylons. Triggered ability defense boost reduced by 10/15%.
If Unsuccessful: Pylons absorb your ship's engine power, increasing an additional 5% to the defense boost ability.

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Ship Events
With the new weekly mission having a comm transmission, there could be new ones that include choices.
These events will be like planetary events. Our ship moves a lot, right? Those these events are both good and/or bad depending on your choice.

Examples:

Cloaked Appearance
[Incoming Transmission from Crew]: Sir! Our scanners detects a cloaked object of some sort. Scanners will have to go overload in order to penetrate the cloaking fields. Orders, Captain?
2 Choices:
Overload scanners to penetrate cloak: Scanners take damage but the cloaked artifact was revealed as a "Time Manipulator!" (The artifact in quotes can be random)
Leave it be: You choose to leave it be, the object may be useless and scanner damage is not worth it.

Ruined Station
[Incoming Transmission from Crew]: Sir! Our navigators have spotted a ruined station. Heat sensors detect no signs of life, but one of our officers swore he saw something move in there. Proceed to investigate?
2 Choices:
Investigate with 10 crew members: 10 Crew members are sent to explore. Only 8 come back alive, but they have retrieved an archive of data. Grants 2 hours of research, can exceed cap.
Ignore: You see some shadows as well and decide that it's not worth exploring in risk of your crew members' lives.

I like some of the ideas, and if it was on a widespread scale I suppose the ship events could work, I'm not sure as to their benefit though. I mean scanner damage for a TM? Is there a chance to get rare artifacts out of this or even the occasional gp arti? Like a terraformer etc.

Interesting, I like it

two hours of research for 2 crew members? wow, that's spectacularly not worth it.