How about adding a system that enables boarding? After researching marines or equivalent technology there could be a possibility for researching some means of boarding - boarding torpedoes or assault shuttles with breaching charges etc. This should require that the ship has a marine module, similarly the ship getting boarded should have a good chance to repel boarders if the ship has its own marine module. furthermore a large ship with module should have more marines than a smaller ship with a module.

If a boarding action is successful there could be all kinds of positive options, from being able to use the ship to being able to research counters against that races tech e.g. improved EW could be researched giving an advantage against that particular race.

Several counters could be researched aside from having a contingent of marines on board e.g. an automated defence systems module or a self destruct module destroying the ship if it falls to boarders.

  I think that might be a fun addition to the combat system, what do you think?

With respect.