I remember arguing about this before my, ahem, absense.
The changes made so that an AS can no longer effect a ship with a damaged MC make perfect logical sense because a ship with an MC has no crew to convert. However, if a ship's MC is destroyed then that ship should be dead in the water instead of being able to continue to fight with a movement penalty.
The change so that AI's will always use the MC if they've researched it is way too heavy-handed. We're going to see some odd, and very expensive, AI ship designs.
It looks to me that the AI in general just got handicapped and psychic AI's just got screwed.
Other than those issues the patch seems great.
(I don't want to be totally negative!
)