Okay, I've tried that mod that barnes suggested. It's helped with the meshes and textures, but it seems to have affected the balance of the game as well as having messed up the AI.
Ships now just fly into impassable objects (like planets and asteroid fields) when given an order to move somewhere or to return to a shipyard. They also seem to ignore the standing orders you can give them, things like "fire on sight, but don't move without an order".
The worst part of the now dodgy AI is with the artillery ships. You tell them to fire at a target in range and they'll try to move right up close before firing, making them useless against anything stationary that could kill them like turrets or star-bases.
I don't seem to have much luck with mods xD