Okay after some bits of thought, (and a rewatch of Sweet and Elite), behold my list of ponies and my opinion of them.
1. Rarity - Like Season 1, Rarity continues to dominate when it comes to being my favourite pony. Now that they've established her character a bit near the tail end of Season 1, it seems that the writers have managed to work their way around with the character and not only play to her strengths but allow for Tabitha to bring in remarkably dynamic performances. Out of all the characters, I was exceptionally worried if they would ruin Rarity by simplifying her character to stereotype. But thankfully, they didn't and she comes out the most well-rounded, dynamic, multi-talented (Fashion designer AND Barber) and vibrant characters of the show, and so much so that I believe she is the only pony of the Mane 6 that can have a strong stand alone episode to herself.
In a way I find her to be kinda like the Osaka (from Azumanga Daioh) of the Mane 6 in the fact that is a sui generis character, a class of her own. Whereas Osaka was a new class of flake, Rarity is a new class of fashionista.
In short it still remains that Rarity 4ever.
2. Rainbow Dash - RD kinda grew on me this season (as well revisiting Season 1 episodes). She has quite a bit of great reactions and pieces to her name, and her focus episodes (aside of course from MMD, which is just some separate microcosm that best be forgotten) show her to be quite fun and quite quirky. You gotta hand it to her in episodes like Hurricane Fluttershy, where she is able to work on levels of loyalty, determination, guts and what have you. She rose up a bit for me.
3. Twilight - She's become quite a bit more adorkable this season indeed. Her spotlight episodes were very good, and her presence in a lot of the episodes was well-used and not very shoe-horned in. Her reduction in presence kinda stopped her from being too oversaturated, and Tara Strong continues to know how to make her well... Twilightlicious.
4. Applejack - AJ knows how to grow on you. Even though she's in the majority of the season's episodes, when she's not even a part of one I kinda feel something's missing without her down-to-earth poniness. She knows how to remain the most consistently written of the Mane 6, and her two episodes this season were high points to be sure.
5. Fluttershy - Not gonna lie, Fluttershy I find to be much more overrated than RD. Her demureness is endearing but quite frankly in light of the other three before Rarity she was just pretty good this season. That said, she was quite exceptional in her two main episodes. I dunno, this seems like a good place to put her.
6. Pinkie Pie - Shame really, but Pinkie really kinda dropped down a bunch from being Number 2 last season. I think it's just that here, her episodes were remarkably weak in their own way and despite all the gags and Smile Smile Smile it shows that they seem to at times put her antics before her character than vice versa. That leads to episodes with relatively questionable moral values like A Friend In Deed to episodes which could've needed bit more exposition and pacing like the MMMystery on the Friendship Express, which again mostly focused on antics. Cute antics to be sure, but still... Antics before character.
Well that was hard. I like everypony, but... here's my ranking.