I'm unsure if this is the right place to bring this up, but it seems like the best place.
The one major annoyance I've encountered so far is with the confusion effect in combat, and its interaction with the auto-attack AI. Basically, if you have a confused party member, and some other party member defeats its current target, the confused member is then eligible to be auto-attacked by the now idle member. It is also quite easy to accidentally attack the confused character if you are used to selecting characters by clicking on them. This is frequently the worst consequence of the confusion effect, which otherwise seems mainly to leave the affected character idle.
This doesn't make much sense. It is the affected character that is confused, presumably. But the effects are more like the entire party is now confused about the allegiance of the confused character, and will gladly attack him/her. Is it not possible to remove control over a character without making them a target like this?
