Personally, I would like at least two different auto-attack strategies... One as it is now, and one where they only use the base attack.
More times then not I find myself wanting to use auto-attack to get through the first 1 or 2 stages of battles, but I can't because I want to save the special attacks until the 3rd stage, and of course the current auto-attack will always use special abilities first. Hence if I use auto-attack then there's a good chance my abilities will be in refresh moe when I get to the hard battle.
I really think there should be more user configurable auto-attack strategies in place then just the one. I find the current mode really bad for most battles and have had things like heals going off when my entire team was over 75% health.
Looking for allies level 40+