Here goes my top 10 of favourite ponies, no matter if they're main, secondary or BG. And because I have a lot of free time, I'll say why:
10. Princess Luna
Some will say "heretic!" for putting a royal princess in the last position, but the lack of character development made me choose that. I know you'll say "but Berry Punch doesn't even talk, so character deveopment is no excuse", but the lack of Luna during the Royal Wedding gives me enough reason to say that.
9. Octavia
She's in ninth position for a single reason: her color scheme and her fancy style makes me want to see her speak at least for once. Of all musician ponies, she's the best in my opinion (yes, even better than Vinyl Scratch. Don't judge me, bronies)
8. Rarity
How come the fanciest mane pony ended up in 8th place? It's simple: She had too much screen time in S2 in my opinion, thus leaving the others (except for the Cutie Mark Crusaeders and Rainbow Dash) with less chance to have character development.
She has a good personality, she's generous, she's fancy and looks after her friends, but selling her plot for more plot was unforgivable.
7. Queen Chrysalis (not a pony, but I still put her in the list)
I'll be honest with you: She's the best antagonist so far in my opinion. Why? She physically looks like a decompsing pony (like a zombie), she used an army, or swarm, to invade Canterlot (the swarm looked like a zombie horde), and most importantly: She has her own song.
I know her motivation was a bit cliché and overused, and I know Discord has more fans because of his personality and John deLancie, but her attack on Canterlot is the losest thing in the show that resembles a zombie apocalypse. You may not know, but I'm kinda obsessed with zombies even more than I am with ponies.
6. Derpy Hooves (Ditzy Doo for those who have been bronies long enough.)
How could I dare put such a cute charachter, the favourite among the fandom, in the sixth position? She's the pinacle of fan service: her name, her first lines, her derped eyes, etc. Don't take me wrong, but fan service is not always good.
Do not misunderstand me, though. I'd also like to see an episode focused on Derpy as long as she's not portrayed like a pony who causes nothing but accidents. I like to portray her as a clumsy pony who just have bad luck and is naive. You like Derpy? I like Derpy, but that doesn't change the fact she's a fan service pony.
5. Fluttershy
What can I say abou ther that you don't already know? She's kind, she's cute and she can forget her shyness when her friends are in trouble. The problem is: most episodes focused on her are similar: make her be more assertive. You don't believe me? Then rewatch Dragonshy, Putting Your Hoof Down and Hurricane Fluttershy
4. Berry Punch
Why is a background pony in 4th place? Easy answer: the fandom. She's either portrayed as an overprotective mother or a drunken pony (mostly the second), and I like that. It's not that I like to see a pony being drunk, but it's the jokes that come up with it. It's tough to explain clearly why I like this BG pony so much, but I do and this is just my opinion, bronies.
3. Trixie (aka The Great and Powerful Trixie)
She just showed up in a single episode (and was mentioned once in another episode), she caused nothing but trouble and she apparently didn't learn a lesson about not being boastful. Even though, she's my third favourite pony and I can explain clearly why.
She has unique personality and color scheme; she speaks in third person most of the times; she has strong magic and fandom loves to make her either confront or befriend Twilight Sparkle. You got to admit she has more personality and character development than most one-shot antiheroes like Flim and Flam.
2. Pinkie Pie
I'll say why she's in second place with just a couple of reasons: she breaks the fourth wall and she's an unconventional pony. Also, she sings one of my favourite songs: The Smile Song.
One more thing: I truly dislike the fanon personality she was given because of an infamous fan fic. She's not phsycotic, for goodness' sake, she's the type of pony who always want to have fun with friends.
1. Twilight Sparkle
My highest priority pony since I became a brony, that's a fact. There are tons of reasons why she's in first place, so I may miss some:
She's smart, she's surely the most magical unicorn, she's a bookworm and she's extremely organized. Some will say: "so what?" Well, what I don't often say is that her personality strongly resembles mine and because of the show I also found more bonding and the little thing that is called "friendship".
Belive it or not, this show changed my life, and Twilight Sparkle had a lot to do with that change.