@Latecomer
It’s complicated.
Part of the fun was that the show was better than it had any right to be. It felt like we had discovered a hidden gem of a show, and were getting away with something by watching it.
I think a lot of Season 1’s “greatness” was something the fandom projected onto it. For example, I don’t think the lore and worldbuilding started to get good until around Season 6. That being said, I think 1 is still the most expertly-crafted season of the entire show.
Overall, I felt like the show got better the more rules it could break and the more risks it could take. But Season One had already happened, and the magic of discovering The Mane Six and watching them become friends was something the show couldn’t exactly repeat. To that end, my favourite seasons, in no particular order, were:
Season One
Season Five, for finally going to the dark, emotionally satisfying places I always hoped the show would go.
Season Eight. Everything just sort of came together, while also recapturing the magic of discovery from Season One.
I’ve said that the 6-7-8 era was “A show called ‘Friendship is Magic’ is actually about characters becoming friends.”
That’s just my take. Someone else could give you a different top 3, with different reasons.