The main problem I see with WoW is the lack of group content, yea there are raids and dungeons but that is just not enough. I would say this is the biggest problem in every single mmo made post FFXI, devs are making Solo player multiplayer games... (my biggest game breaker of mmos, I just despise solo mmos)

outside that I would say these are my major issues with it:

1) Craft system is horrible (click a button 100% success, crazy easy to level up)
2) Everything is designed to let you win and rewards are handed out like candy at Halloween, makes some people feel good but it is a rediculously shallow experience which leaves you with no sense of accomplishment. The All reward no work. Nothing is epic if 90% of population has it.
3) Updates destroy all old content... cataclysm made almost everything if not everything in WotLK completely worthless for endgame.
4) Tiered gear for everything... FFXIV actually has this and I am very weary if this will happen in throughout the game if it does it will be a massive negative that FFXI did not have. This leads to people not doing lower level dungeons, NMs, and raids because the gear will be gimp in 4-5 levels, and is a big culprit of #3.
5) The game throws Gold at you... FFXIV has this to an extent as well but no where near the level WoW's quest do it. You can afford anything just by doing quest in WoW.

Other things not related to game play which made me hate WoW:
1) Community is the biggest collection of crap I ever seen in 1 location ever. (ask for help on a quest and you get 6 replys calling you a noob or worthless trash because you are attempting to do group quest... seriously WtF)
2) The graphics where subpar at launch. (It has improved over the years but the polygon count and texture details are horrible)
3) I do not like the art direction (Looks like I am playing an upgraded more mature toontown) This one is all personal opinion though.
4) Being locked into 1 class.... This was my biggest draw to FFXI over EQ back in the day. No idea why mmos keep doing this but I view it as a cheap way to keep you playing the game.. being forced to play the whole game 6-10 times to experience all the possible classes.