Yes, there are, and I can tell you what the problems are:

1) Blizzard rushed the release of Cata, thus, a lot of content had to be left out. It turns out all of that content was Alliance content, since Blizz decided to work on the Horde side of things first.

Therefore, the Alliance intro quest to TH got dumped in favor of Fargo's whacky ride. The Worgen were supposed to get their own district in SW where the park used to be, and from there go questing in Duskwood, etc. Instead, they left a f*ing hole in SW and shipped the worgen to Darnassus where they get green and grey quests, their story left unfinished.

2) While the Horde was supposed to get more territory this expansion to compensate for the Alliance advantage in Vanilla, Blizzard overdid it. Southshore was supposed to be destroyed by a tidal wave, they changed it so that it was bombarded by the Forsaken plague. The whole Forsaken expansionism is overwhelming, one wonders why they stopped at the Thoradin wall.
The Alliance got no militar victories whatsoever, the only one being Camp Taurajo, that ended up being a guilt trip rather than a triumph.

3) Horde leaders get a lot of developement, specially Garrosh and Sylvanas. The Alliance leaders... hardly any.

4) Questing for the Horde feels like an epic experience. Questing for the Alliance alternates between depressive losses and Pop Culture references.