I started thinking about this in the "crew mechanic" post and I really like the idea of using marines in a more active role during the real-time combat.
The idea is simple, allow marines to be launched via shuttle (or some other transport means, perhaps even have dedicated "breaching" ships) so that they can board enemy ships to carry out missions (sabotage weapons/systems, capture ship).
This I feel will add an interesting tertiary combat method for victory (ship->ship combat, fighter->ship combat and marine->ship combat). Suddenly those large troop transport ships become a lot more useful in combat for large protracted battles against hardened battleships, where you are going to need a lot of marines in order to disable targets or capture them.
Obviously missions to capture ships would be the most difficult (risk aside from being shot down en route), but it does reward persistence and more tactical play (I was thinking an anti-personal weapon type for ships could help soften up enemy ships by killing their marines/crew), and being able to focus your efforts on the ship you wish to capture would be pretty cool (rather than having a random chance that the ship you want comes up post-battle).
I think the tactical possibilities are pretty good. Send marines in fast shuttles to disable escort ship weapon systems so that you can then send in slower larger troop ships (perhaps something like that dedicated breaching ship) to attempt to capture or disable it's lethal armament so that you can move in your ships to finish it off.
Of course you will have to deal with the same problems, so protecting yourself with dedicated anti-personal gunships, or point defense weapons becomes a higher priority.
EDIT:
Ignore this post, I'll delete it after you all have had a bit of a laugh (since I didn't read the frequently made suggestions!)
