On the origins of magic in MLP: FiM

If you really wanted to be pulling at straws and give a pseudo-scientific explanation, you could probably say that the essence of life that exists of its own accord (i.e. sentience) and its subsequent perception of a physical reality could be in a sense, a form of magic, since no other organism can experience another organism's perception directly, thus allowing one to "change" the fabric of reality from the singular viewpoint one possesses.

Okay. So back to MLP. If I had to guess I would propose two sources.

First, a generic "fantasy" sort of magic that comes from life, or crystals, or deities, or the sun, or something. In this case, it's a kid's show, so we don't need to get into details there.

Secondly, if we wanted to reach into epileptic trees territory, one could probably justify the theory that Equestria is a post-apocalyptic Earth tens of thousands of years after humanity (and thus the EqG portal is a time machine rather than a direct portal. Bam!), and the magic and anomalous effects we see (cutie marks et al.) are actually the results of biological nanomachines produced in the horns of the unicorn variety of ponies.

The ponies themselves are genetic mutations of animals. Because of the docile and friendly nature of horses and the lackadaisical and slacking nature of dragons, the ponies with their powers of flight, strength, and magic, outlasted most of the other forms of life, and because of their genetic mutations (read: genetically modified to have sentience) created their own society based around their in-borne genetic abilities.

You could explain the strength and communication-wth-animals abilities of the Earth ponies with basic biological engineering of muscles, and the signalling of pheromones to other animals in order to gain their trust.

The pegasi, despite their small wings, actually use nanomachines and arrays of millions of microscopic static air fans embedded in their wings to fly. They control the clouds via electromagnetism radiated from their static fans, and the clouds they lay on condense at points of contact because of the EM field.

The unicorns use massive amounts of nanomachines to lift objects, change their molecular structure, or mutate other living things by infusing them with nanomachines.

I really got carried away with this theory. I actually like it more than I thought I would as I was writing it.

Anyways, yeah, magic is kinda arbitrary and nanomachines are cool or something.