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S1: Green Isn't Your Color. Love the conflict, Rarity's self-aware jealousy, Photo Finish, the "forever" gag… such a solid episode.
…or maybe The Best Night Ever, for six simultaneous stories and all that climactic anticlimax and introducing us to two Wonderbolts.
S2: Hurricane Fluttershy. Flight training. Rainbow being awesome and straining to be supportive. Fancy pegasus weatherwork. Science and measurables. Fluttershy's pain and justifications for her weakness. Final triumph without making Flutters into supermare.
S3: Magical Mystery Cure. Musiclicious, and ♥ Rarity's weather patterns. Twilight's ascension, which comes when she is ready but before she thinks she is – story-wise, the perfect time. The coronation scene is shitty, though.