In hindsight, alicorn Twilight was inevitable since at least the beginning of the second season. First season largely and happily avoided any of the grand narratives that have choked our media for decades, but the second-season premier ended in a giant Star Wars homage.
Star Wars, of course, is the point at which Joseph Campbell’s concept of the monomyth entered Hollywood’s consciousness, and it soon came to dominate. The Hero’s Journey is obnoxiously omnipresent in modern Western television and film, and by heavily referencing Star Wars, MLP basically announced that the foul spectres of Lucas and Campbell had taken up residence in Equestria.
And how does the Hero’s Journey climax? Usually, with some combination of ultimate battle between the hero and evil/repression, the acquisition of the treasure the hero’s been seeking (knowingly or unknowingly), and apatheosis, the ascent to a godlike state. Either of the latter two is obviously the transformation into an alicorn, and the first could be the trigger that necessitates that transformation.
Now, oddly, the series isn’t ending here. There’s a few possibilities. One is that the Return phase of the journey involves an unusual amount of conflict, and the next season will cover that. Another is that Twilight must choose whether to sacrifice her newly gained power and knowledge in order to Return, and we all know she’d choose to restore the status quo. The last is that, as is often the case with female Hero’s Journeys, the journey is cyclical, and either Twilight or her friends must complete more journeys in future seasons.
I hope it’s one of the previous two. The problem with grand narratives is that they are predictable and tend to make all works that share the narrative similar. MLP is an unusual and special show; it shouldn’t be constrained by having to fit into a storytelling cookie-cutter from Film 101.