Cryptic has suggested that ship interiors will be coming down the pike eventually and there's been a lot of discussion about missions that take place on your ship. I've been thinking about the way the general nature of the game and trying to think of Star Trek episodes that involved shipboard missions that would fit in with the nature of STO.
One that came to mine was the episode "Starship Mine". This is the TNG episode where The Enterprise D goes to the Remmler Array for a baryon sweep. Everyone has to leave the ship because the sweep is harmful to living tissue and would kill them. Picard returns to for his saddle and interrupts some bad guys trying to steal trilithium resin from his warp core. The whole episode is basically a shoot 'em up cat and mouse run from one end of the ship to the other always trying to stay ahead of the baryon sweep.
Talk about a mission perfect for STO and ship interiors!
You and your away team could work your way from one end of the ship to the other fighting the bad guys you encounter along the way and it could culimate with the boss fight in the main forward lounge. If they could add in the aspect of the sweep advancing behind you (effectively adding a timer constraint to the mission) I think it could make for a fun, possibly even challenging, mission in STO. And it all takes place aboard ship!