After PvPing for a bit, I've been reconsidering Horde vs. Alliance. I still think that the Horde have a slight advantage when it comes to mobility, and that Paladins are a little too vulnerable to interrupts/fear/shiny distractions. But for the most part, the factions are reasonably balanced against each other in PvP.
However, on average, the Horde are still better than the Alliance. As Horde, I win far more games than I lose. I think that this is because the Horde gets much more practice than the Alliance.
If I'm only on for an hour, as Horde I can get in three to four games. As Alliance, I'm lucky to even get one. So the average Horde gets a lot more practice at the BGs, and thus gets skilled in a faster time than the Alliance. I would estimate that a Horde Rank 6 plays as many games in a week as an Alliance Rank 10+.
As well, the fast queue times allow you to experiment or incorporate new ideas faster. If you have an idea to improve your play, you can instantaneously test it out. If it's a bad idea, and you lose the game, it doesn't matter, because the next game is right around the corner. The feedback cycle is much faster, and thus you can improve your skills faster.
As they say, practice makes perfect.