I know I have more ideas/fixes, but I can't remember them at the moment. They can be added later.
Bug: In Ironwork Munitions Factory's second stage, floor 16, it is possible to get get your teammates stuck with no method of escape. In the area shortly after the start, where you move down and trigger 3 switches to fight quicksilvers, there is a small area to the right which often contains a treasure/heart box. If someone hits the switch while the rest of the team is there, the rest of the team is trapped with no way to get out. They can only go back to Haven after the switch-hitter leaves.
Bug: When you have an armor equipped, and a costume armor equipped as the costume, there is still the option to equip the same armor cosmetically, which results in an error on the server (as it attempts to switch armor and armor costume, but the costume armor does not have stats).
Being able to select 10 materials at a time would greatly help in trading. It can be the same method as adding 10 minerals at a time to a gate (ctrl+click, I believe?).
If people could simply receive all items from Auction House mails, it would save the tedious amount of time for people to open these mails when buying multiple materials for crafting (or when selling such materials).
It would be preferrable to have a warning box option for joining people (from friend/guild list), to prevent accidentally leaving dungeons/wasting energy.
Apparently these ideas are less popular than daydreaming about new equips, bosses, and balance changes (altho balancing is feasible)?