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.)