Miss:
Talent trees. I enjoyed being able to play weird specs (hemo/swords anyone? SL/SL lock?) that sort of worked. I also think that no matter what people say about them being cookie cutter, there WERE terrible specs and it let you at least know if that person had a brain or not.
Difficult 5-man content.
No connected realms/cross realm instances. I know this gives you convenience, but at the price of accountability. And you should never sacrifice accountability. The vote kick system does nothing to help. I would caveat that the new "tourist" mode LFR is probably an exception. That's meant to give crappy gear and just be an easy thing to do. LFR within a server would probably not work.
Raid attunements
What I don't miss:
Having to relearn abilities when changing specs
No dual-talent spec