It would be cool to come across Neutral ships or utility vessels like mining or transport ships and have an option to "hold them up" or destroy them. Some would be much weaker (not outfitted for combat) but attacking them would reap some benefit to the player at the cost of moral righteousness and infamy.
Obviously there might be some cases where the player will want to play as a "good" Captain, but circumstances might lead to desperation and stealing from friendly vessels might be your only option. Other times you might just be ruthless and need to pillage from whoever you can you achieve your primary mission.
I would like to add that something I don't like in games are things like paragon/renegade bars in Mass Effect. The only thing your choices in the game should matter to is how NPCs react to you and treat your actions. If you make a bad name for yourself, pirates should be less inclined to cross paths with you and other ships should be less enthusiastic to help you.
Here's an example of how "moral choice" events could play out (underlined is chosen option):
- You arrive in system and detect a pirate ship attacking a mining barge. The barge is badly damaged with inferior weapons and requests help:
- 1. Target the Pirate ship
- 2. Target the Mining barge
- 3. Open Comm channel with Pirates
- 4. Warp away
- *player engages and destroys pirate ship gaining x scrap and x fuel another menu appears* <you did a "good thing" so the barge will want to reward you and positive fame is earned in the galaxy>
- The barge is now alone in system. You receive a hail from them:
- 1. Open Comm channel with Barge
- 2. Target the Mining barge
- 3. Warp away
- *player engages and destroys barge gaining x scrap and x fuel* <you did a "bad thing" which overrides whatever morally decent thing you did saving them from the pirates>
In that above situation word might then spread about your renegade actions and situation might arise where ships could attack you who would normally not or less trade options would be open to you.