Realistically, any of the Houses could win. It would depend mostly on the competence and strategy of the 'Field Commander'.

4166139
Then, some foreign power might come in and take over instead.

i think that Everfree has the best chance at surviving this whole mess. they already live in a self sustaining enviroment, all they have to do is put up a policy of "We don't attack you if you don't attack us." and wait it out. when one House, or cult, comes out the victor they strike before they have any chance to build up. Of course they'll still have to deal with Earthborn but still.....

4492715
A sound strategy that can be used by the rest of the five, there are reasons why they don't do that. From the looks of it, Everfree expands continuously, most likely towards Earthborn to the south (The Frontier) and Stormwing to the west (The Northern Expansion), Old Ponyville of the centre being flooded and cannot be claimed.

At this point, Earthborn and possibly Stormwing would want nothing but destruction to the Everfree because of their general attitude, their culture. Kill or be killed, invincibility lies in the defense, but victory lies in the offense; if they don't fight, their war will never end and their losses will be great.

Eh. I'm more along the line of CMC Alliance leading to the destruction of M&S. In the end Equestria remains divided for several generations, eventually the crazy dials down and they join together in some sort of new-monarchy. Everfree stick to the forest.

Really though I think once the Mane 6 start to die off the emotional freight-train will start to peter out.

Personally, at first I would have imagined Spike eventually managing to escape from Twilight's control and forming his own faction to end the War, but now I'm not so sure...

I mean, out of all the Groups, either the Cult would win if nopony stops it, or eventually the Windigos will come AKA Winter Is Coming...

So far, the only hope would be a possible CMC Alliance...

No one but the dragons would win in my point of view they all wipe each other out that entire kingdoms won't exist anymore but as a memory and Equestria and the world will become quite places with only dragons being largest race left to rule.

Every faction and nation will lose and be wiped out leaving ruins and ashes the world where Equestria is located at and the lands around it well be empty with no one to clAim it. And a lone male earth pony collector My character Telwyn Freecolt well learn and study the old world of Equestria and lands around it collection all he can find learning all he can of the world before.