Eh I don't know.
Storywise: Their both pretty good honestly, their backstories show multiple shades of black, grew, white and orange which I like. But the horde takes the cake for having a great redemption story, plus, they have thrall.
Races: Hard one, Orc's are cool looking, so are tauren and the trolls. But blood elves are anorexic bastards (which sucks because their back story is awesome.) and Goblins are annoying.
On the Alliance side humans are...well human, pretty well done though. (Guys are way to muscled though and females always have very big...wings? (An internet for anyone who gets the reference.) Night elves are strippers, Dwarves are really cool, gnomes suck period, the space goats are cool but to "good" and the Worgen are freaking awesome (If anything for the british accents)
Leaders: Back when Thrall was running things it was horde hands down but now that its Garrosh the horde is screwed (Especially since Cairne died and Sylvanas finally lost her mind) on the other side Varian is a horrible man in my own opinion but Jaina is pretty cool and Aundrin Wyrnn is awesome)
Overall: Back in the old (Pre-cata)days its horde hands down but now I have to say Alliance as their starting to actually become good and the horde is becoming Xenophobic. So yeah, Alliance