As I hit 90 this afternoon I decided to post a few of the things I am not really liking about the expansion. Be aware, I still think it's way better then Cataclysm, as most of the issues I had with Cataclysm have been fixed. However, nothing is perfect, and there are some things that could use some work.
Leveling
While the leveling feels more consistent then Cataclysm, it still feels like it takes a long time to level. Maybe once I play one of my better DPS classes the leveling will speed up, but even compared to Cataclysm is just feels awfully slow (this might also be a side effect of not having a flying mount). Personally I think they should reduce the requirements by another 20% and decrease monster health by 25%, so that it does not feel like I am beating down a monster for ages. Will it happen? Not likely, but I feel it would help. At least they didn't go through with the even more steep experience requirements from Beta. This gets into another issue.
Zones
One of the things they were promoting was a more variable leveling path. They even went so far as to split a zone to add another one during Alpha. However, they still suffer from the fact that only one level has a "choice". 86 allows you to choose Krasarang Wilds or Valley of Four Winds, but after that suffers from the same problem Cataclysm had, which is forcing you to pretty much route through the same zones, Kun-Li, then Townlong, then Dread Wastes. The reason for this? They decided to remove Vale of Eternal Blossoms as a leveling zone and instead made it a daily quest zone. Sadly, this removed a zone option. However, don't take this as a horrible downside, because Blizzard did stick to their promise of making more hubs in each zone. This means it's not entirely linear, and you can pick and choose questlines a little bit better. Still not as good as it could have been.
Reputations
This is probably my biggest problem with the expansion, and I am still scratching my head about it. All the JP and VP gear is locked behind reputations. At first I figured this wouldn't be too much of an issue, however in order to get to the main gear reputations, you have to get Exalted with the Golden Lotus, and only then do the other two main ones unlock. Really, starting out, the only reputation you can start leveling quickly is the Klaxxi, and that is only because it's one of the few factions that actually gives you dailies starting at 89, while also giving you reputations for general quests (lots of quests in other zones don't give any reputation at all). This, combined with the fact they removed the reputation tabard, means you likely won't unlock the JP/VP gear for a few weeks. Considering the JP gear is only 450, while the heroic drop gear is 463, means no one going through the game normally would in the end need that JP gear. This will probably lessen a bit when the VP gear downgrades to JP during 5.1, but I still find it a bit odd to do.
Alts
Really, my issues above in the end root to this problem, and that is MoP feels very "alt unfriendly". The long leveling can make it difficult to stay focused on the character, adding on the fact that this expansion decided not to go through with adding any new heirlooms for the 85-90 range (they added some pants, but those are only for 1-85). The fact all the gear is behind reputations means you can't just play a little bit and slowly JP yourself a decent set, and depending on how many characters you have, means you will have to do a lot of dailies. This is not going into the fact Spirits of Harmony are BoP, making it difficult to viably level up alt professions.
Once again, don't get me wrong, the expansion is still much better then Cataclysm, and my hope is that by 5.1 we get something to make alt leveling a little easier (I admit, Rested Experience will help a lot at least). This expansion, if you have one focus character, is well crafted with a lot of personality, but an altoholic like me feels a bit like my preferred playstyle (having multiple high level characters) was a little bruised.
