This is a awfully old post, but i think i may have a theory as to why this could hold some truth
I want to begin by stating that this will contain a theory on equestria being founded millenniums after the events that take place in gen 3 and 3.5, and this theory is based on a time line that spans 1000's to 10,000's of years.
Lets begin with the geography, since there are many similar areas to equestrias (and beyond) layout vs the lands of old gens. Lets say, equestria is the same world as all the other areas in the other gens, but at each point in time where we see each generation, the world has changed due to climate and moving plates of their worlds fault lines, similar to how ours did when we had super-continents. with our gen 4 being a super-continent itself.
with that in place we now look back in equestrias history, as far back as the three tribes. i believe the separation of the pony tribes after gen 3-3.5 were originally caused by climate/continental changes, maybe something in tune as an pony ice age, which would bring the snowy north where the yaks and crystal empire are today to light as they are the last of the snowy past of to which we see in gen 4, and at this start of this ice age, many different ponies started to fight against themselves,for resources and food, which caused a rift to begin, and thus bringing in the wendigos, which until the unification of the three tribes occurred started each pony waging wars against each other fighting for survival with all ponies fighting against each other no matter what race they were, which could have span throughout many decades. this would occur until the 3 tribes came together as unified tribes, where all pegasi supported pegasi, unicorns supported unicorns and earth ponies supported earth ponies, which started the wars against the tribes we knew occurred at one point. This would lead to what we all know would happen with the three tribes coming together and unifying at the first heartswarming eve against the wendigos before everyone froze to death at the end.
As for the reasoning behind why there no humans in gen 4, we look to the eqg portal, maybe there used to be a portal to a human world that was in the older gens that was destroyed or something happened by the time gen 4 came around, and that the eqg portal is a nonfunctional-malfunctioning portal that sends ponies to a human-hybrid world since it isnt fully capable of send them to a full human world