Lack of a proper instanced housing system (single rooms don't cut it)

Lack of 3-axis free placement in housing (short of using tedious floating and storage glitches)

Lack of 3-axis rotation in housing

Lack of server wide opt-in housing directory to make it easier to find houses and apartments to visit

Lack of corresponding updates to friends list (so if someone removes a friend from their list, they are removed as a friend from that other player's list)

Lack of a content unlock mode for players not interested in the story but that would otherwise enjoy much of the game play

2.1-2.3 (I'm fine with 2.4 and 2.5)

Expert crafting still needs a more engaging reward system

Too much fanservice that ends up detracting from the game instead of adding to it

Probably a few more things I can't think of off the top of my head

[but I'm still enjoying the game overall despite the flaws, no MMORPG is perfect]