My thoughts, in no particular order
* limited number of landmarks, and limited edit capabilities. Lack of colors for better visibility.
* risk of data loss wrt local files.
* not being able to activate an action with the craft window open (e.g. self focus) due to the modal dialog.
* unsorted inventories at login
* tell windows taking the focus away. You are typing in around, and suddenly all your interface is messed up because you got a tell.
* limited number of hand bars.
* timer for auras/power ups a bit too high.
* faction channel bug (can't type in it)
* faction channel not appearing in user tab.
* offline players can't be added from freinds list. Remove works but you still get a message.
* special mention to some bugs
- wrong info message, kick of team
- speed on daggers