Letting ally ships shoot through eachother and bump but not injur eachother seems a but limiting.
You could have an option to turn friendly fire on/off so to increase the dificulty and realism.
Also with regards bumping off or drifting through like ghosts i think bumping off much better, however in a lot of games that this happens in you can get ‘stuck’ or ‘cornered’ and not be able to move temporarily, which suck! So you could have an option like ‘shock em’ which activates a charge that bounces nearby craft/ships away with minimal damage to them , once your shocked you become inactive for a short period of time. You only have so many shocks to use during game play abd more can be bought/found/awarded.
Powerups that increase firepower and speed etc are always good, and they can run on a countdown forcing you to make use of them before they run out. This would really kick a slow game up a bit and make inactive reluctant battlers be forced to go for it.
Capturing the opositions equipment as hostage to use against them is also always a winner.
Rather it just being two sides against eachother maybe also include a sub mission like something that needs finding and the side who finds it first gets rewards of weapons/coin/craft etc.
But yeah the friendly fire thing could be an on off option and bumping can be made interesting by the ‘proximity shocker’ idea 
Got loads more ideas hit me up if interested