I agree. First are you playing Supernova and patched to 1.6?
You may want to turn on Fast Move late game. This should resolve the issue. The problem is the game animating all of the moving units. With fast move this becomes pretty zippy.
Regarding the End Turn issue I'd like to see this changed as well. On a turn if you press end turn, the yellow triangle. It will resolve all queued movement. If any units have move points remaining after this it will allow you to spend them. Then it will automatically end turn after this.
Instead, I'd it require you to hit End Turn again after you have used up all of the movement points. This should help. I haven't seen end turn
I'm guessing instead of minor races you mean pirates, monsters and sentinels. Minor races are the yellow ones. I believe only Crimelords have this issue as of 1.6 with Supernova. Before there was a Criminal Ties ideology that prevented you from attacking pirates.