Now first, here is the fanfic I wrote myself: http://www.fimfiction.net/story/343429/guiding-light
The premise is rather simple: An earth pony filly (named Aurora) lives in Canterlot, and despite reforms, tribalism is still prevalent. This is made worse, as she has an interest in studying magic. She is constantly bullied by her peers, but things change when she stumbles into the Crystal Caverns underneath the city. She finds a small, hidden study full of books, books for the instruction of earth pony magic, something that had previously only been taught through experience and guesswork. Even then, such magic was passive.
If I say much more, though, it will give too much of the story away.
And on to recommendations!
Alarm Clock, by Meta Four: http://www.fimfiction.net/story/56774/alarm-clock
This is a story about Ditzy Doo, or if you want to use her full name, Detsella Renombrada Morningdew. Her special talent relates to dimensional travel. Shenanigans ensue. (No, this fanfic does not include humans.)
There is a story, but I can't tell you any of it because of spoilers. Sorry. But it is great, and you should check it out. It is possibly the best Derpy/Ditzy fanfic out there.
Rites of Ascension, by CvBrony: http://www.fimfiction.net/story/39849/rites-of-ascension
This is a big one. 59 chapters, and over 400,000 words, and it still isn't finished. But it is worth it. It is set in a canon where only the first part of Season 3 happened. In fact, the author himself hasn't even seen any other episodes, until he finishes the story.
This is a Twilight ascension story, and in my opinion, it does it in a better way than the show does. It creates well-established canon about magic and related magical artifacts, and the story accurately simulates pony politics without boredom. In addition, it has an overall story arc that is complex and mysterious, while having mini arcs that are fun and exciting to read. The lore alone is fascinating enough, and there is even a separate "Rites Encyclopedia" that explains the canon if you missed it in the story, and don't want to go back trying to find what you missed: http://www.fimfiction.net/story/153395/the-rites-encyclopedia
Oh, and Alarm Clock has some pretty great sequels, too.