Well I have found that often my flagship gets deployed on the wrong side of the map which can take 10-30 seconds to properly reposition at the start if there are big slow clunky ships involved to get them in the right places, Its not a huge issue, but I have wanted to be able to re-organize the starting deployment layout prior to Initiating combat. (assuming the player is in a position to do that, pursuing a fleeing fleet, and trying to bust through a blockading fleet should dissallow this as thereisn't time for proper redployment, but the less rushed confrontations should allow you to pick where the ships come in from.
Given Alex's hints on map borders lately and the possibility of deployment form the map sides, this may be something we'll get in time anyway, it certainly would be nice to have control over deployments which is finer than "Lets all charge down the middle Lol!"