Lets talk about this for a moment from two points of view, lore, and logical progression of game mechanics literally speaking.
Lore:
For a while now the faction war theme has become somewhat a stale, dying thing, after the events of Stormhiem it is obvious that the -last- embers of that fire are slowly burning out while end game pvp events still exist across the world of small skirmishes.
The conflict between Alliance and Horde cannot last any longer, the continued fight would only end with the Legion winning if any division lasted, which leads me to believe inevitably, the factions must unite.
Many of the groups within those factions are all but ready to work together, and with every class basically ignoring the war itself in favor of a common unity against a single foe, it seems logical to assume, the war will end permanently.
But who will win? If there is a winner?
Taking this Logically: Who started it, who will finish it:
The Horde essentially began this fire with an inavert betrayal from Sylvanas Lieutenant Putress, whom gave Garrosh the fire he needed to start a real war agianst the Alliance. Unfortunatley at the time, Varian had not yet learned the value of diplomacy and peace, and didnt do anyone any favors by running straight into the fire himself, eager to see the Horde burn for its -betrayal- of the Alliance, a reoccuring theme in most storylines.
In Cataclysm, that conflict went Nuculear when Garrosh ended what little truce there was with the Alliance against the Lich King, and expanded purely for conquest sake, while Deathwing was beginning to destroy the world.
The Horde has basically gained massive victories during that time, most that gave it huge swathes of land and territory, but it did one thing wrong that has slowly come to haunt it ever since.
It united the Alliance.
Up until that point, the Alliance was a divided order of individuals that had no real common ground, they were driven by individual politics and problems in local borders, refusing to help each other at the call.
Then the Horde drove them together, and the Dragon that shattered the world, Deathwing, only amplified their unity.
Ever since, the Alliance began to become stronger, and stronger, until when the mists of pandaria conflict escalated, the Horde had a civil war thanks to Garrosh finally going too far.
This civil war fractured a war-unified Horde into two sides that essentially crippled its own faction from within, that faction has constantly suffered ever since, with its conquest driven victories quickly turning into a shattered dream of domination.
Warlords gave the Horde a small comeback, a break from the fight while the Alliance mostly had the brunt of the Iron Horde invasion, but the Horde did send its own troops to Draenor to take what riches it could, and to secure the aid of the AU Orcs.
This has bought it -some- troops back but not enough, the reality is, the events of Stormhiem have now -damned- the Horde, as Sylvanas and the Undead now have no real future because of them with Genn having annihilated the one real way the undead could have continued to -exist- unless she decides to align herself with the Legion.
This concludes that the Horde, is the defeated party, right?
Not necessarily, not -quite- but the Horde -will- change thats for sure.
Jaina is a factor and wild card in all this, and Genn too, the rage of these two chars may boil to a point that the Alliance ends up having its own civil war, enough, that it might cripple it from within. This would be the opportunity, the Horde needed as an equaliser to stand once again against its rival.
However...
The Horde is a tired beaten animal that has suffered quite a few gnashes itself. What it needs is not to end, but to unite, the Alliance will ultimatley become -both- factions, and the Horde will -become- part of the Alliance when the true conflict between the two is entirley over.
This seems all but inevitable, as events are now being set in motion that pull away from the tradition of factions, and step forwards into the creation of the Army of the Light, as Velen's Prophecy foretold in Cataclysm.
Aside from Lore, mechanically, we are moving into that age:
The ideas of faction pride will always exist, but I think its universal to say -most- people are slowly fading away from the purely psycho-patriot view of alliance vs horde mentality with the constant neutral enemy theme. Its a tired old trend that needs to end with a side winning, or both sides changing into one bigger side.
It also offers opportunities that are denied without it, the ability for blizzard to develop new races without fear of faction loyalty, the ability to create guilds without a boundry of side, the ability to raid/dungeon and experience content as one side rather than as two.
However, there could still be ways to make the boundry exist:
The Old would not be thrown out just like that:
Old racial specific content would still be relevent via legacy content, such as old dungeon revisits and raids, being locked to a specific factions old racial loyalties so if your Horde race, you'll still get the Horde story for certain raids.
Same for Alliance.
For older leveling content, the general flow would -still- be about the factions, allowing people to at least experience the story building from chapter to chapter as they eventually become one with their rivals and understand the transition that lead to it.
Over-all, there is no need to remove whats already there, but rather, to add something new to what isnt.
To open the door to a bigger world and stop being afraid to embrace it.
Its time to stop living in the past, and start moving into tommorow. The next real stage is a battle beyond alliance and horde, but a battle of good vs evil, perhaps, the future will have us not just joining together to form the army of light, but perhaps even being tempted by the Legion itself, to create an entirley -new- conflict, between those loyal to the alliance/horde army and those that betray it for the power of the demons and their ilk.