I agree with you totally, however, you could just not use the autocast and do it yourself... or we have to make the artifical intelligence much more smarter.
As far as i know, the AI use the same autocast we do, so if we make autocast smarter, the AI will become much better. Besides, micromanaging become a pain as our fleets become larger, and certain units are used in large numbers and their abilities just get wasted because the faulty autocast. No doubt we can always do it better, but i'm sure you agree we can't alway be there to make sure...