I have decided I don't think making the ai use missle ships will help eliminate this problem. I can still beat any ai with equal CSM tech level by simply timing my shots right.
A better solution would be to go back to the way SEIII made you research to get CSMI. If it was not a default tech then I wouldn't be able to use it so early. No matter how good I am I am going to take damage in a DUC to DUC combat. Sometimes will even lose if the ships are equal.
This would allow the ai some time to build up more colonies and or research CSM and PD weapons. At the very least he could build more ships. Then when I do come at him with CSM's he won't crumble to the weight of my mighty CSMI single escort blockade fleet.
