I think -first of all there should be a ship anti marine weapon.... (like the death ray from master of orion 2)
-second marines should be movable i.e your get a new ship and want to transfer the marines from the old one.
-third the mothership should act as a reserve post for marines, so that your ship can resupply without taking money or when your out of money.
-fourth marines still on a dieing ship should be able to use esacape pods to move to a remining ship after combat - if mothership is there then marines would board that instead..
-err the one after 4 (how do you spell 5 as a rth)a system that inscreases the defense rating of marines. like the computer does for acc and def.. could be called war room, security station etc etc..

these are idea's ive had about marines while playing this game ( its good by the way)