the Alliance had a storyline focus. That is, Arthas and Bolvar.
However, the Horde actually got a far BIGGER military advantage.
They got the Taunka, Proto-Drakes and Magnataurs.
The Alliance got sweet nothing. So in terms of military strength, Horde won WotLK as well.
Now, we move onto Cataclysm.
The Horde dominated almost every single zone.
And the thing is, blizzard have admitted they WON'T be re-doing the old world again.
This means these changes are permanent, pretty much. So to those saying "Oh, it's not fair if they get owned in MoP, they should win THEN lose." I've got news for you - They've been winning for a long time. Give the Alliance some muscle flexing, perhaps?