It would be wise to start out as Horde first and then factioning over to Alliance as you would be missing out on a lot of useful gear that requires Horde side to obtain.
Items such as Merger Boots, Uninsured Bracers, Stillwater Signet, Argas Ring (for x2), Wild Rider Glove's, and Shield of Talrendis.(hope I'm not missing anything). These are all BIS and there are really no significantly better items on Alliance side.
Despite the fact that you would be missing out on those items listed above, if you do decide to stick with Alliance there are always some items that will suffice and won't effect your game play.