Again, my argument is that the Equestrian ponies, in reality, would not look anything like they do in the cartoon. And that the cartoon versions are very highly stylized depictions of them, similar to anime depictions of humans. Keep in mind the style of the artist who originally created them. MLP ponies are done very much in the style of Power Puff Girls, which Lauren Faust was heavily involved in. And like MLP ponies, Power Puff girls, although vaguely human in appearance, bear little actual resemblance to what real humans look like. I tend to feel that MLP ponies are the same way.
The fact that I'm an evolutionary biologist by education also plays a role in why I think that way about it. There are too many evolutionary problems with the canon ponies. For example, no creature that lived above ground would evolve eyes that large, unless they were completely nocturnal. They wouldn't be able to see anything during the day because their eyes would gather too much light. That's just one of the evolutionary problems with the cartoon style ponies given the environment they live in.
Call me cynical, but personally I think the main reason some MLP fans (mostly in the teenage / early 20's male demographic) have problems with realistic depictions of the ponies is because so many MLP fans in this demographic view the ponies as not much more than sex objects. And realistic depictions of the ponies tend to make them feel a little bit too dirty about that.
In fact, that's one of the primary reasons my own art depicts them in a realistic style. To make people stop and think about what it really is they love about the ponies. Is it just the fact that they see them as sex objects? Or is it something more meaningful? Like their personalities, their moral values, and their friendly natures?