Auto explore (4 Intermediates!)
Any good player (good player = a skilled opponent in competitive multiplay) will tell you not to use Auto Explore. Get in the practice of clicking your scouts around manually early game while you are waiting on things to build. Scouting is pretty important in this game, you'll want to know what your opponent has and where it is heading to best move your fleet to attack and defend.
A great trick, I play alot of 2v2s online, is once your scout has reached an opponent's homeworld and surrounding planets, do the following: Select scout in question, zoom the map out, hold shift and start right-clicking all around the systems in his locale. In other words, set up many waypoints criss-crossing your opponent's territory and your scout will scoot around giving you very up-to-date intel without any further inputs required.
Turning on auto-explore is like buying your scout a one way ticket to the pirate base. Next game, travel smart.