Hi. I've come up with a theory based off of the trailer to Equestria Girls, assuming that the information is canon. This could actually give us explanations for MLP:FIM's universe.
Infinitely many universes exist, planes layered one on top of another. Each soul of an individual intersects across each universe (like a line, creating parallels of individuals across universes), each soul except the Alicorn souls, which only exist as a point in a single universe (combining all parts of the pony into one also concentrates souls). This explains why there is a human vinyl scratch, etc, when only Twilight has gone through the portal. When a soul becomes an alicorn and the line becomes a point, it leaves all universes but one: it can only exist in one at a time. All other universes "forget" this soul, a space-time hiccup occurs, and the universe continues as if the soul never existed to begin with. That is one of the power of proper application of the Elements of Harmony.
Evidence at this point for this claim: http://i.imgur.com/6RVkl7d.png
The advantage to being a point-level soul, or an alicorn in this case, is the ability to retain consciousness while traveling between universes. Opposed to being entirely different individuals, or lines passing through a plane, you are a single point, a single consciousness, with the ability to take on different values, or points, defined by the plane you are in.
All this is well and good, but why was it imperative that Celestia make Twilight into an alicorn, if it was stated by canon sources that Twilight is not immortal? What reason did she have? I have another theory based off of other people's theories: One of Celestia's students prior to Twilight, Sunset Shimmers, was made into an alicorn and traveled across planes. She was similar to Twilight in that she valued education, and immediately came to explore the educational system of the new world she was in, learning about its physics, mathematics, etc. However, this world was strictly non-magical, and she couldn't return. In an attempt to force herself back, she had to fight the laws of the universe, which she could not do. Her magic, which should not have existed in the first place in this universe, but was a part of her, (as she was a point not a line... and I'm guessing it was really powerful magic too, as she was one of Celestia's students), instead of returning her to Equestria, created her own universe. This one is its own plane that intercepts these "soul lines", and as such will have parallels of all individuals in the other ones. It is created from only what she experienced in the world: High School, and governed by its laws. As in the human plane, magic does not work here normally, but there are loopholes, as it is not an exact copy of the human plane, only one made up of subjective experiences of a magical creature. Soon Sunset finds that she can manipulate the plane to a degree, living in a paradise of sorts, where she is the popular girl, the one thing she could never be while growing up an introverted genius. Here she lives out her fantasies.
Celestia does not know her reason for not returning, as her knowledge of these planes is limited. She trains Twilight the best she can, as the other alicorn princesses are needed to rule the current world and cannot leave, in magic so that Twilight can be prepared for whatever she might encounter in the other worlds. She finally turns Twilight into an alicorn when she feels Twilight is strong enough, and sends her into the other plane to retrieve her lost student.
Here is where the movie begins. Twilight lands in a high school setting. She finds that the universe is completely centered around one being: sunset shimmers, and that the school consists of the entire universe. She finds her friends in this universe, as souls they are also in this universe with different memories but the same essence (RD is still loyal, for example), and befriends them again. She learns from experiences that this world is governed entirely by high school, that there is something very wrong and that this is not the actual human plane, but a different planar universe inserted between Equestria and the real human plane. She eventually discovers the truth: That the entire plane is an construct of Sunset Shimmers, and that only Sunset can leave it. However, Sunset is living in a paradise world, and doesn't want to.
Meanwhile, Sunset Shimmers discovers Twilight has entered her plane: a new girl who she has never met, with mannerisms of a pony, and puts 2 and 2 together. She was Celestia's former student, she isn't a dolt. She can logic it out. She guesses Celestia sent Twilight to get her back, and doesn't want to go back. So she makes life terrible for Twilight, as this is her universe and she is in control.
Now how to get the universe out of her control? Prom queen (essentially. I forgot what it was called). By making Sunset Shimmers no longer the most popular girl, you will do two things: You shatter the illusion. She is no longer in paradise, no longer wants to stay, and.... You gain control of the universe. This universe was created by certain laws, laws that Sunset learned from only one experience of the human plane: high school. The queen of high school, therefore, will govern the world.
Now with the help of her friends, Twilight eventually earns Prom Queen, restoring Sunset Shimmers to her original, mentally stable state. She sees the error of her ways and the universe collapses, ejecting the two points and making it as if the infinite number of soul-line intersections never existed to begin with: the individuals of this universe are gone now. They no longer exist, as they are intersections across a plane that no longer exists. Twilight and Sunset end up tumbling through the mirror (a dimensional gate) and end up in Equestria. Celestia congratulates them both, and now there is no longer a "wall" of sorts, (an intermediate plane) between Equestria and the human plane.
So, what do you think of my explanation? Better than a cheesy high school drama?