I saw someone else suggest this once and thought I would bring it here. The suggestion was to get rid of the guy or girl that would show up at Traffic Control when you warp between sector blocks and replace them with one of your Bridge Officers doing the pop up. This makes a lot more sense than haveing some over arching traffic control watching all the boarders in the game. Ideally, the pop up to warp message should be your Navigator or Helmsman on board. Since we do really have a way to specify these characters, I suggest taking the Engineering BO (or better, the lower level one if your ship has two.) Generally Helm has been operations or Command. I could also see a tactical officer in this role. Either way, have them pop up to ask if you want to warp to a new sector block.
(Personally I suggest that there be a way to appoint crew to specific "positions" on the ship independant from the BO stations. But that is another topic.)
I have also noticed when joining a battle already in progress, that a random ensign is generated to ask us to continue exploring or leave the sector. I'd rather see one of my BO's consistantly deliver this message.
Additionally, I've noticed that while space missions are usually delivered by the appropriate BO, away missions are usually delieverd by a BO that I happen to have selected for the away team. Sometimes, though, I get a lower-ranking ensign delivering the message, which I find to be more appropriate as they would presumably be the most senior officer remaining on the bridge. It would be nice to see the latter consistantly as it not only makes more sense but it involves those lower ensigns which more than likely do not see a whole lot of away team action (being less developed).