I'm sure all of this has been mentioned, but:
Hood Toggle
It really bothers me that with certain characters - the Guardian and the Shadow particularly - I have to either wear social/gear intended for another class or sacrifice armor rating in order to *see* the character I created.
Appearance Options
I still feel extremely limited in my appearance choices, due to the high price of extracting endgame armoring/mods and the limited number of armor models utilised for each class/armor type.
Spike Lag in Operations
In Denova, particularly, 2-3 second lag spikes across the ops group are frequent, frustrating and will likely be crippling if we ever see a Nightmare mode Denova.
Companions, Class Content
At endgame, companions feel like robots, it's easy to forget what your character sounds like (especially when it comes to content like the Grand Acquisitions Race, which doesn't include any PC voiceovers at all). I can't be alone in wanting more class content.