The only main thing I can think of to compare having auto-attack or not is this:

Being able to chat while battling. Currently, you don't really have time to do anything except click the mouse button, the 1 key, or the enter key/confirm button on the gamepad over and over. If we have auto-attack, sure, you might be able to let the character battle for you if it's not too demanding on your TP skills, but at least during that time you can chat with your linkshell or friends, or heck, even have time to take a bite out of a snack you have. You can reply to a text you get during a battle. I would rather have a few seconds of free time in between TP skills or job abilities to be able to reply to something in linkshell chat, rather than be forced to click 'attack' over and over and miss out on conversations.

I think having auto-attack would let you have more fun and more freedom. Just my own opinion, of course.