These are my top 10 favorites (in no particular order):
>Trixie
I honestly didn't like her very much back in the early days of FiM, probably because I thought of her as just a generic meme character. She really started to grow on me in recent seasons as she started to be fleshed out more and be paired with Starlight in a lot of episodes. They did a good job of keeping her personality intact without flanderizing her. She's a better example of the "arrogant, self-obsessed show-off" type of character than Rainbow Dash, because they writers normally try to give it some sort of foundation with Trixie. With RD, it's typically just "Dash acts like a cunt for no reason again".
>Sunset Shimmer
I could write several paragraphs on why I like Sunset so much (I'm a bit biased, admittedly). I think her most distinctive character trait is how she's the closest to a "real person" of any of the main characters. The writers have historically been very willing to take her character into areas where more "picturesque" characters, such as Twilight, Fluttershy, and Pinkie Pie, have almost never gone. Sunset is not the sort of bubbly, cartoonish person that we expect to see in MLP. This ends up making her more relatable and more sympathetic when she does slip up every now and again.
>Maud Pie
Remember when Maud was first introduced and Pinkie talked her up to the M6 as a fabulous, well-rounded character, only for them to be be immediately put off by the "muh rocks" bit? I like how that has retroactively become a meta-joke about this character. People who want to think that Maud is just a meme character will always linger on "muh rock autism". However, Maud has gotten a lot of characterization in every major episode she appears in, including her debut episode. Yes, the rocks thing is still there, but it's no longer the only thing you expect from her character.
>Rarity
Rarity is another character I wasn't really that fond of at first. I used to think she was too much of a one-note character, because she wasn't given that many moments to break out of her "muh dresses, darling" niche. However, I think she has gotten some terrific development over the course of the show, more than anyone else in the M6 by far. She easily fits into almost any episode these days and almost always makes shit better when she does show up.
>Applejack
Applejack used to be my favorite pony. I loved the simple country girl thing she had going on for a while, which was helped by the writers actually giving her stuff to do other than just working on the farm. Unfortunately, she got flanderized to hell and back as the show went on. The "appuls" meme has finally become a reality, as she is typically just used as a walking "dumb redneck" joke whenever the writers have the generosity to give her a speaking role these days.
