One thing - recharge times on Planet Sculpting Tools, please remove.
In-fact, two - the cut scene when going through black holes gets rather tedious when you're going through them a few times.
Three - were proton missiles actually tested when Spore was in development? It's just that they are no way "Effective against enemy spaceships." one's that are flying away from you anyway.
Four - not enough control with cargo hold, would like to see a sorting feature or manually being able to move things around (without having to drop them on planets and pick them up again).