In no particular order
1. Freeform jumping with tasteful limit via a jump stamina bar.
2. Freeform swimming with breath bar. Both this and #1 involve re-doing zones to have less invisible walls.
3. More interesting combat animations and spell effects.
4. No more screen dimming when others perform a weapon skill (is this still in the game?)
5. Support for custom UI creation. This does not imply addons like threat meter/whatever, but those would be cool too.
6. Side quests that emphasise story in the same way main quests do.
7. No limit on solo leves (this might require adjusting bonus earned while solo). Limits on leve linking can stay. Goal oriented solo content is very important.
8. More solo options for combat classes besides leves and grinding (and arguably behest). Behest for hamlets, attacks on beastmen tribes and not just camp defense, escort quests, etc.
9. Full crafting recipe book, creating items from recipe book without drag/drop items into craft box (last 8 recipes is not enough).
10. Dramatically sped up gathering pace. Too much text happening while gathering. Put more focus on the animations and less on the text. Combat and crafting classes can go by animations alone; gathering classes can't.
11. Removal of stat allocation cooldown OR stat allocation based by class, not by physical level.
12. Auction house. Market wards still blows, can't fix it without turning it into an AH, stop wasting time on it.
13. Mail system.
14. Emphasis on teamwork during combat with a group, emphasis on self-combos while not in a group. I don't know if both are possible, but if not, emphasis on teamwork during combat should take priority.
15. More class specialization. Classes too homogenized.
16. Travel options besides running and teleporting.
17. Pankration
18. Dramatically less copy paste and monotonous zones. West Thanalan looks identical to East, North, South, and Central Thanalan. Same for every other zone. This needs fixing ASAP, when zones are both huge AND monotonous, they have no charm and nobody likes them.
19. Armor customization via re-dyeing and remodelling.
20. Alt-tab while using full screen client.
21. Definitely need beastmen or some sort of evil presence in the game, especially early on. Got to level 20 and everything I did felt unimportant. I have no goal.
22. Chat channels; trade, general, LFG, etc.
23. Automatic bug reporting. i.e. when the game crashes, the client asks me to automatically send in the crash report to SE. See WOW and RIFT's automatic crash report feature.