Loading the colony list (Civ Manager->Colonies) can become very slow, especially with textures enabled; buying a building from the list requires a complete reload of the list, over ten seconds in some cases (but this is only an issue with hundreds of colonies).

The AI never colonizes PQ 1 planets, which typically have a terraformed value of 10-16 PQ. Neutral AIs or those with an orbital terraformer should realize this.

The AI never sends a transport to a colony with a ship in orbit. Building a dummy ship every turn effectively prevents the AI from invading under most circumstances, even if it is killing the ships every turn. The AI should be able to attack and follow up with a ready transport the same turn, or have transports fleeted when it expects to win space combat. (The AIs are "Genius"; is this the smartest type?)

What is the intention of the Mind Control Center? I've heard that it gives +100% economics as an undefined value, but is really supposed to increase flip frequency of planets. My observation is that it gives something equivalent to +100% loyalty to the enemy. It makes the already powerful evil AIs even worse (or the player if evil); if it simply gave an extra flip roll for planets each turn to the controlling player it would help to balance the alignments. This would have to be my top fix for the next patch (if the current behavior was not intended by design, as most people believe).