If we were focusing on Finales and Premieres only, I'd say Magical Mystery Cure is one of the best season endings. It really encompasses the spirit of the show (friendship), I'm a sucker for the music, and it would have been a perfectly good ending to Twilight Sparkle's journey since that's what the show was from the beginning. I'm not asking for the show to end, but I know all good things eventually come to an end, and I'm always kind of wondering which season will be the last and final season of MLP:FiM. Magical Mystery Cure was one of those endings that would have been just perfect if the 3rd season was the final season.
However, since this poll is strictly about two-parters, I'll go with my second choice; Twilight's Kingdom. And I'm not just saying that because of the epic battle with Tirek! It doesn't have as much memorable music as Magical Mystery Cure (to me, at least), and the plot could have been a little better... But the ending really sold me. Like Magical Mystery Cure, if season 4 had to be the last and final season, that ending would have been just fine to end it on. Friendship unlocked a new power for the mane six, you could argue it's a better ending for Twilight's personal journey through the series, the spirit of friendship ultimately helped save the day and brought everyone closer together, and it just felt like a really nice book end.
All the other finales after that have been very different. While they would be a good way to end the series completely; they actually make me want to see more. The Cutie Re-Mark really made me want to see more of Starlight Glimmer and see what her reforming would mean. To Where and Back Again makes me want to see what Equestria will be like now that the Changeling race has been reborn with new leadership and such.
Also, sorry if I'm not giving enough love to the premieres. :sweat: I like a lot of the premieres too, but I feel like it's a little unfair to compare them. Premieres represent the beginning of something, and Finales represent the end. If you must compare them, it's only natural for me to gravitate towards endings because everything has been building up towards them. With finales, there's usually more conversation material than there is for premieres. If the finales and premieres were just as mundane as the slice of life episodes, it'd be easier for me to maybe pick a premiere I like more.