When there are obstacles in the way, ships seem to be very horrible at finding their way around them and at not running into them and coming to a dead stop. This is particularly a problem for capital ships.
Very very quick replay. My capital ship is ordered to phase jump to another planet. It comes out of the capital ship factory and stops itself on the weapons lab. And stays there. For about a minute. Its orders are to phase jump but it just sits there, perhaps waiting for the structure to be destroyed or something, thrusters on full while apparently attempting to move "through" the structure. At long last the ship figures out that it can go underneath it and, after a few stuttering stops along the way, makes it past and starts moving towards the edge of the gravity well.
This sort of problem happens way too frequently. Say I have a capital ship that jumps into a neutral gravity well. I order it to move to the other side of the gravity well. There happens to be a planet rock (extractor asteroid) in between. Does the ship avoid it? Often times no. It will often simply run into it, come to a halt, and then eventually figure out that it has to turn in a different direction (z-axis often) in order to maneuver around it. This can waste 20 seconds or so, more if one isn't playing on Faster, and even more if the neutral militia are mobbing the capital ship like they normally do.
This can be very significant, especially in more competitive games against humans where seconds matter a whole lot in the early game.
Can we have ships whose captains are not criminally retarded please? Players would probably appreciate it a lot.