Winning
I enjoy playing Sins enormously, but I always find winning such an anti climax. There you are working hard to crush the last AI, and suddenly you're pitched into the win screen.
One change I would like to see is an option to explore the universe a la Age of Empires. It would be good to easily look around and see what remains of your enemies, and what remains unexplored.
Again looking at AOE the last AI always gave some feeble excuse for resigning, and I think it would be good if you got a whisper from the AI offering surrender or withdrawal or something before you're pitched to the win screen.