This finale. Wins everything. This might be a long post, and it will mention previous MLP series (G1 mostly). Everything stated here is my humble opinion.
Twilight's Brother coming out of nowhere seemed incredibly shoe-horned at first, but I think the writers did a fantastic job explaining that with Twilight's dialogue about how far away they drifted.
Cadence didn't have such luck when being explained into the story. 'She use to babysit Twilight' doesn't hold water as being a good explanation of her appearance and we know nothing more about her then that. Clearly this added Alicorn felt like an excuse for pretty pink princess toys, but at least the episodes were good enough to brush this thought aside.
The beginning was somewhat slow going, and I blame not having any real emotional connection to Cadence OR Shining Armor for most of the first episode. After the usual introduction and easing into the plot, things get really good. REALLY good. "Twilight just got engulfed with hellfire and dragged to the bowels of the Earth after tearfully apologizing to an evil enchantress" good.
Part Two was the best thing ever to come out of MLP, bar none. Chrysalis (A script page of the episode named The Changling Queen Chrysalis) has to be the best villain that has been introduced so far. She looks beautiful and deadly, was far more effective at her job then Nightmare Moon, and I found her more interesting and more dastardly then Discord. Chrysalis was deadly. And her name holds so much meaning.
Best part of the whole thing were the songs. Finally we get a proper villain song.
Regarding Luna, I found her pretty funny in the finale.
"REST, MY SISTER. AS ALWAYS, I WILL GUARD THE NIGHT."
"TWILIGHT SPARKLE, YOU SHOULD BE INSIDE."
"Hey guys, what'd I miss?"
I think the writers knew how little she appeared in the show and lampshaded it at the ending with her nonchalant pointing out she missed the biggest most epic fight at that time.
Also, DJ PON-3's eyes are more purple then the red I wanted, but still. She was pulled out of thin air by Pinkie! So great!
I will probably add more later.