I may as well put them in my order of favourite to least favourite. I love them all though, so it doesn't mean too much.
Rarity
My favourite from the very first episode. I always prefer feminine characters, and Rarity is just that. She's essentially all my favourite characteristics rolled into one; she's funny, classy, creative/artistic and can handle herself just fine. I also love the fact that she cares about her appearance and looking good, but she doesn't act like it makes her better than anyone else. She enjoys being beautiful because she appreciates beauty, not because she wants to be superior to anyone, or links beauty to importance. She also has great character development. Unlike Fluttershy, who forgets what she learns about being assertive by the next episode, Rarity's lessons on being cooperative with her sister and the likes actually seems to stick with her. I also like how she's a little more contested with her element. She is certainly generous, but sometimes it clearly clashes with her vanity streak and that makes it more interesting than the others, who seem to fit their elements without any problem which is boring. I like to see characters work and struggle for their achievements, not have it handed to them naturally.
Pinkie Pie
I love Pinkie Pie. She's so happy, all the time, and it's inspiring. I have used her outlook on life as personal advice before and I always feel better for it. Her happiness is so innocent and genuine that it's hard not to love her. She's also very selfless, always doing what she does to make everyone else happy instead of worrying about herself. I've never been one for "random" humour, but Pinkie pulls it off well without it feeling forced. Same with her cheerfulness, she does it without being cheesy.
Rainbow Dash
Like with Rarity, Rainbow is confident. I love confident characters, I can't stand the meek, far-too-modest-for-their-own-good type. I love Rainbow for her reliability, mostly. She can make fun of her friends almost to the point of mocking and pull pranks and whatever, but at the end of the day she wouldn't ever ditch them and most of what she says is just a joke and you know she doesn't mean to be malicious. Reminds me of one my friends, I suppose that's why I like her so much. I also find her fangirling somewhat relatable One thing I don't like, however, is that Rarity gets grief for the same things Rainbow should, but doesn't. People complain that Rarity is obsessed with beauty, but ignore that Rainbow is obsessed with looking cool/awesome. Both are shallow, really. But that's irrelevant to my thoughts on the character, just wanted to throw it in there.
Twilight Sparkle
Twilight used to be my least favourite. Just found her so bland and typical 'main character' fodder. But, after I rewatched some episodes, she really grew on me more, especially after the sleep over episode. She can be pretty funny as she usually plays the 'straight man' to the other characters. The way she always likes to do things by the book and on schedule reminds me of myself, too ^^; However I don't really like how OP she can be. I know magic is her talent and all, but... I dunno, just makes me think of the likes of Superman, who usually is seen as boring because he can do everything. A lack of limitations really ruins a character for me. She's not that bad though, yet.
Fluttershy
I don't think she's all that cute, for starters. She has a pretty design and she can act cute, but I think the fandom has grossly exaggerated it. She's not really cuter than any of the others, they all have their moments. Anyway, Flutters is just too simple for me. She's shy and good with animals. That's... really it. She has little else in the personality department. Oh, and she's kind. Two very, very broad personality types and a rather generic (for a cartoon) talent. All of her episodes are the same, too. All the other ponies learn different lessons in each one, but Flutters only ever learns about not being so shy and not being such a pushover. Important lessons for sure, but do I'd like to see her in different situation. I'd also like to her actually learn from them too. I dunno, I like her and all, she's cute and kindness is always commendable, but there's just far too much hype for such a plain character.
Applejack
I want to love AJ more, I really do. She's awesome, and her basic traits (honesty, hard working) could be interesting to see more of. But she just has hardly any development compared to the others. Even Fluttershy got more than her. And it's hard to put an under-developed character in the same category as a developed one without creating your own headcanon and stuff, which I don't like to do. So until we get to see more personality for AJ, I can't rank her higher D:
The only other pony I can be bothered to write about is Cheerilee, so let's go!
Cheerilee
Cheerilee is a personal favourite because I'm training to be a teacher too. I sort of look up to her. She's a good teacher. She's fun, her students love her, she's kind and caring and yet she's able to be firm when she needs to, so she keeps control of the class too. Teachers in cartoons are usually portrayed as awful people who hate children (yet are in schools for some reason) and usually have it out to punish the students. Or they're shown as sleep-inducingly boring. It's nice to show a teacher that the kids actually like. I hope I can be a great teacher like Cheerilee