It's controversial to say, but at the beginning of WoW most good players interested in PvP went horde. Generally the alliance had a softer, more feminine image and the horde was full of badass ugly people so obviously it would appeal more to angsty young guy wanting to stab shit up. No surprise, in vanilla and TBC, horde was the completely dominant faction everywhere except AV ( and even there it was only 40-60 or something).
Not a lot has changed in that regard. Alliance still have a very "Disney" image that would appeal to female and younger players, and the horde still have the badass image (excluding blood elves). Since the best pvp players overwhelmingly tend to be young men, it stands to reason that the faction that piques their interest will be stronger in pvp.
I should add that for much of TBC, Wotlk, cata and MoP, alliance had superior pvp racials. There's nothing inherently better about the horde, it's just a case of which demographics prefer which faction. Demographics are a huge deal in WoW which people overlook; the same reason why rogues are ever-present in high level pvp despite having the lowest population and irrespective of patch balance, tends to be because the demographic that plays rogues is very different from the one that plays... for example hunter or druid.