While the final episode of the last Season had Twilight undergo a physical transformation, this was the season that had Twilight mentally grow from someone who's trying to find her place in Equestria to an official member of royalty. Also, R.I.P. The Hub.

5.Rainbow Falls — Guess even the egotistical Rainbow Dash can have doubts, as she juggles between training with her Ponyville team (consisting of the anxious Fluttershy and the muscular Bulk Biceps) and the Wonderbolts.
4.Maud Pie — Ah, Maud Pie; Pinkie's polar opposite of a sister. She's so emotionless, yet so lovable.
3.Simple Ways — We all know how much Rarity hates getting dirty, so seeing her step out of her comfort zone to impress a stallion was hilarious.
2.Pinkie Pride — Pinkie Pie meets Weird Al Yankovic; do I really need to say anything more?
1.Power Ponies — Who doesn't love a good superhero episode?

Disclaimer: These "top 5" images are my opinion, so you're free to agree or disagree with them.