I would say one of my biggest pet peves with the game is how the AI "intellegently" surrenders to another empire when it is certain its war against me is lost. I always proceed to conquer that species colonies as if nothing happened (which declares war on the empire that accepted their surrender, even if they are my allies they will not be spared).
Moving in on your spoils of war in such a manner is unacceptable, there should be stipulations:
1. If the empire estimates its military might to be weaker then yours after the merger it should not accept the surrender.
2. The AI should never surrender to a civilization more evil then you, and infact, shouldnt even surrender to one just as evil (since you will exact retribution...)
3. If an empire is allied with you it should not accept the surrender.
etc.
While seeking the protection of someone strong is reasonable the AI usually performs suicide through this method. (the one who gets the surrender not the one who surrenders)
Oh, and the AI should consider surrender earlier then when its totally crushed if it has a close ally (ie, it will join up with its close ally)