Ah yes, the mysterious barren wasteland. The big question going around is "Who or what caused it?" I initially thought the windigoes might have had something to do with it, seeing how barren and stormy everything had become - both telltale signs of the presence of windigoes. After all, Eqestria could easily have grown bitter and cold without friendship, possibly bringing back the windigoes in the process, since it's implied that the Mane Six never came together at all in this timeline, let alone activated the Elements of Harmony. The main problem with this theory is that as far as we know, the windigoes were completely eradicated long before the timeline was altered. Not to mention, there's no ice in sight, which is what windigoes in Equestria are best known for, as it's what causes the aforementioned wind and famine. That being said, the idea of the windigoes returning could make for an interesting story in the future (after all, there was a subtle hint at the possibilty of them still existing at the end of Hearth's Warming Eve, so it's not too unlikely that they could return, given the right conditions). Then, I figured it might be the result of what could have happened if the parasprites devoured everything and later went extinct because they ran out of food, ending all life in Equestria. If that's the case, it just goes to show how one polka song can make a world of a difference! However, upon further observation of the map of Equestria, something stood out to me. In every timeline (including the non-corrupted present), the cyclops skull in the Arimaspi mountains and the castle in the Dragon Kingdom across the Celestial Sea are fully intact and prevalent, even when everything else looks desolate and abandoned. Because of this, I think I might have figured it out. I believe the dragons are the ones who caused it. After all, without Fluttershy keeping them away, they could have easily invaded Equestria. Considering how close the Dragon Kingdom and Griffonstone are to each other, it's plausible that they followed the same route Arimaspi took from Equestria to Griffonstone. This would explain why the cyclops skull is still intact, since that's where the route would lead them, with the dragons hoarding everything in sight. It also provides the best explanation for why everything is is dark and barren: The dragons are covering Equestria with their smoke, hence the reason why ashes are being blown everywhere. In fact, we almost saw this happen back in Season 1 during the events of Dragonshy.
A lot of people are saying it might be caused by a new villain we have yet to see. The main problem with this theory is that if it was the result of a new villain, it most likely wouldn't have happened yet. After all, we are only seeing an alternate version of the present. Therefore, the only way for a villian yet to be revealed in the future to be responsible for it would be if something had caused said villian to take action earlier. I find this very unlikely and hard to believe.