With all due respect, Princess Twilight was foreshadowed since Episode 1:
She was the only one with a crown symbol for her element (in other words, she was the one, like Neo). She stepped out of her comfort zone (left her hometown) and lead her friends against Nightmare Moon and defeated her (slayed the dragon), recognized and enabled the Elements of Harmony in their true form (Deus Ex Machina, seizing the sword), restored the friendship of the Alicorn sisters (resetting the biggest and most tragic upset at the time) and she was the only pony who had direct access to The Princess of Equestria (ie, Luke Sykwalker and Obi Wan) to further and fulfill her purpose/destiny (which the above pic depicts). After Episode two, Twilight Sparkle had changed drastically, and was already worthy of everypony's honor, including Celestia's. When she becomes Princess, she returns home.
Twilight Sparkle is the hero of the show. She is the most influential force for good and decency in the story. There is no other character that has a stronger presence when it comes to the most difficult problems and tragedies. Even when she was written in as a secondary or background character, she is always very close with her council or influence in some way, even if that influence happened long ago (ie, Starlight Glimmer!).
Her hilarious quirks and shortcomings aside, there is no other character in the show with a better resume than Twilight when it comes to achieving the honor of actually becoming a princess. All this has a very plain message - Karma. Do good, be good, make friends, trust, honor and sacrifice, and you will be rewarded.
Luke eventually becomes a Jedi.
Conan becomes King.
The Little Mermaid becomes human.
Neo defeats the Matrix (no more doubts about the prophecy of The One).
etc, etc.
Twilight goes through the same Hero's Journey that almost every story tells. Her becoming an Alicorn makes perfect sense if you look at the evidence...it's just that the evidence is disguised, like most other stories, to elicit the 'ah hah' moment.
The real problem about Princess Twilight is that such an ascension typically marks the end of the story. That's why Return of the Jedi and the other Matrix movies had little impact or reception. But the show persisted...and more importantly, it was expected to persist. And so I truly believe this was the subconscious withdrawal from the idea altogether, and most if not all the criticism of Hasbo stems for this very strong breaking of the rules in our minds.