I really liked from the main ponies Fluttershy, Twilight and Pinkie for some reason.
Maybe because I liked Fluttershy's gentleness and how she knew how to take care of animals. Pinkie Pie was the pony who was able to make everyone smile, and Twilight, to be honest, reminded me kind of myself. I always read books by myself and didn't want any friends. But the fact that she became princess, I thought to myself that she indeed deserved it after all that time.
My favorite villain was obviously Discord, because of how he was intriguing and funny. I always smiled when he was the center of attention. Also I liked how he was reformed and the fact that he and Fluttershy became friends was so heartwarming! Also I liked other ponies such as Maud Pie, Derpy and Vinyl Scratch, but the two of them are background characters only and the other one appeared only in three episodes or so.