This could also open up some fun PVP modes as well. Anyone out there who played Battlefield 2142 probably remembers titan mode. The idea was each team had a large ship and your goal was to work with your team to bring down its shields, board it, fight through the corridors, and work your way to the core, which you detonate.
Seems like that would work fine here too. Ships are tasked with bringing down the Cruiser's shields then beaming aboard and fighting your way through the halls to engineering deck to detonate the warp core. Player and NPC based security teams would try to stop them and repel boarders. On top of that some players could go to engineering and try to repair the shields so to help stop reinforcements from getting aboard.