While MoP was initially build on the idea of pitting them at war (after years of them working together to take down bigger threats) with each other over the course of the xpac they yet AGAIN find themselves repeatedly working together for the greater good, they repeatedly find themselves in instances where guys like taran zhu are telling them that they're being dumb keds and they need to start working together and to let go of all this hatred. We're about to go into an xpac where this 3rd party is yet again going to threaten the whole of azeroth and both factions are looking to stop it from happening because its what's best for the planet.
There have been sooooo many opportunities to do this since wc3 (I didn't play the warcraft games before then) that have the alliance and horde banding together to face some threat. Hell individual races within factions are not at all the best of friends, there's hardly any reason up to this point to keep them separate aside for the sake of keeping them separate because that's how MMO's have always done things.
There is virtually no benefit to the game especially in its heavily instanced form to keeping these players segregated. I wish new MMO's that are obviously not going to have the volume of players that wow has would learn from that and stop following suit for the sake of it and cutting their already small player bases in half.