As a heavy user of auto-pause in IE games, this is one relatively minor feature I'd love to see improved before release. I find it makes parties heavy with micromanagement (like six mages) far more tolerable. Here are a few things that I think should have auto-pause options, in addition to present ones:
Ability readied: Classes like the Cipher and Chanter, which have abilities that may become unexpectedly available mid-fight, would be a lot more manageable with an auto-pause to tell players, "hey, your whatever is now charged!"
Recovery completed: Pausing when the character finishes recovery for a non-repeatable action (i.e. basically anything that isn't attacking) would help to avoid wasting time.
Ability used: There should be better visual feedback for this type of thing in general, but it would be nice to have an auto-pause to alert us that a command was completed. If possible, I would like separate options for spell-type abilities (the traditional "Spell cast") and for special attacks (like Knockdown, Finishing Blow, etc.) so that it could be adjusted to fit party composition.
Idle: This falls under the same umbrella as some of the others, but basically, I'd like an auto-pause for when a character (a) can be doing something in combat, and (b) isn't.
In addition, there are some convenience improvements to the auto-pause system in IE games that I think would be wonderful:
Accommodating simultaneous pauses: Sometimes, for unrelated reasons, I'll pause at the same time that an auto-pause goes off - resulting in neither actually working. It would be fantastic if the system had sensitivity to timing, and could figure out when it shouldn't unpause.
Chains of "Target Destroyed": If a bunch of characters are focusing their fire, and the target goes down, the "Target Destroyed" option will go off several times in a row. This is a little obnoxious, and if possible, I'd like these to be compressed into one pause, indicating all characters it relates to.