In no certain order:
Chat window background with levels of adjustable transparency (I sometimes can't see the fonts at all against the background of the game. Sure you can click in the window to make it dark, but I like using a controller and just glancing at the log to actually see what is there)
I also miss hitting a button on my gamepad and activating the chat window and tabbing through the different chat modes to see what was said.
Ctrl-r without having to hit the spacebar to initiate chat first.
Search. Is there a search in the game like /sea all where you can search somebody by name (or some class) and see where they are at that time? I'm honestly asking because I may have missed it. Forgive me if so.
Same thing for the linkshell chat. I can see a list of members, but it doesn't say where they are. They are simply grayed out if they aren't in my vicinity.
These are the things that struck me during my earlier session. I didn't group or join a linkshell in beta so I didn't think about it until now.