In Endless Space, a simple control was added (it wasn't in the game originally) to process all automoves (without ending the turn), and I think something similar could be very useful ... when you have ships on auto (auto survey, auto explore, or just moving long distance), it can help (especially when you are trying to find inhabitable planets to colonize, or beat the AI to survey an anomaly). I find myself, as I did in GC2, manually controlling some of my ships to further them toward their destination.
