Well, you could write about a time - travel plot in an MLP School of Friendship fanfic. For example, some of the ponies accidentally go back in time to when the school was first being built. They meet the founders and learn about the original intentions of the school. Or perhaps a story where a spell goes wrong and it makes some of the ponies swap personalities. They then have to figure out how to reverse the spell while also learning more about each other. And also, a story about a lost friendship diary that holds the secrets of the early days of the school, and the ponies go on an adventure to find it.
An interesting plot for an MLP School of Friendship fanfic could involve a group of misfit students who form their own club within the school. They feel left out by the more popular groups and friendship circles. But as they work together on their club projects, they discover that their differences are actually their strengths. They then start to influence the rest of the school in positive ways, showing that all kinds of friendships are valuable. You could also have a story where an old enemy of the school tries to undermine the teachings of friendship. The ponies must use their new - found knowledge and strong friendships to defeat this threat. Additionally, a fanfic could focus on a friendship exchange program where ponies from different regions come to the School of Friendship, leading to a clash of cultures and a deeper understanding of friendship in the end.