One thing that would be nice is if it were possible to explore and study those lovely rank 0 hunks of rock that invariably are included in any game. The mechanics could be similar to investigating anomolies, only the planet obviously wouldn't vanish after being searched once. It just seems like a very nice "Star Trek" activity, particularly as it would involve the flagships. Ideally, each world could only be explored once by any race and an away mission would take a ship several weeks.
Just a thought.