I like to see some minigames where they involve the Duty Officers. Say if a Duty Officer was injured in a mission, you can go to sickbay and visit him/her. In doing so, you will activate a minigame, if you succeed, they heal quicker.
Same goes with engineering or research missions. The missions can be passive, like how it is now, but some on board mission can have some minigames added to it for the players to directly contribute, if they want to.
Why not a few more story mission with boarding party on your own ship? Or even more awesome, have EVA mission where you have to space walk outside of your ship.
Anyone remember that episode of Enterprise where a mine was stuck on the outside of the ship and they have to do a space walk to physically remove it? Why not make a mission like that.
Or even like this from Elite Force II: http://www.youtube.com/watch?v=EQEs93kDFLM
If anyone is wonder, that canon in later half of the video is somewhat cannon to the story, they designed it for the Enterprise-E in, I think for Insurrection, but just never used the concept.
Why not even add in infiltrating enemy ship from the outside because they had jam the transporter?