1. Sunset Shimmer -My little pony: Equestria girls: Rainbow Rocks: I never thought it will happen, I never loved someone who was evil, but... this character is something amazing... She not just changed, but she literally acts like she was never evil and trying so hard to be a good friend and is so nice to others. Plus I felt very sorry for her in the Rainbow Rocks movie, how everyone treated her and how basically alone she was (even though Mane 6 were her friends). I have a weakness for this kind of reformed villains. From all the sorrow and her effort to change to be a better person, which she is more than enough and became a good leader of Mane 5 in Equestria girls, she needs to be my TOP favorite character from now.
Twilight Sparkle -My little pony: Friendship is magic: A wonderful character as in personality so in appearance. In the first episode she wasn't likeable to me at all (because of her unwillingness to make a friends), but her dedication and effort always something to learn and her willingness to help anyone forced me to love her. It also seems to me, that she cares for friendship a tiny bit more than her friends and anyone else. She really appreciates friendship and thanks to that fact she became my third favourite. She is very awesome pony.
3. Fluttershy -My little pony: Friendship is magic: So this is my favorite character (as on requested). Quiet, shy, scared, very sensitive, compassionate, she loves animals ... She is just like me! She is my animated soul mate!
This is the main one reason why she is my favorite character from the MLP: FIM. I really appreciate characters like she is. She's a good example for people to be better. It hurts me that so many people hate her -not because of her as my favourite cartoon character, but because her personality is very valuable and I don't understand how can someone hate someone with so much kindness and compassion, which are the most beautiful properties that a person can have. Many characters from other shows are supposed to be kind and sweet, but no one doesn't express it in such a high, valuable and incredible level as Fluttershy does. And real world's missing these properties in many people, that's why her character is so valuable and rare.
4. T.J. -Recess: Because he is the the nicest character I've ever seen. He is so honest, generous, kind, loyal, smart, fair and adorable! :3 I love how he always stands up for everyone -even sometimes for his enemies and I'm always touched by his wise speech... He is totally awesome and wonderful boy. I LOVE HIM SO MUCH!!
5. Applejack -My little pony: Friendship is magic: Although she is not some beauty (unlike to her friends), but her big sedulity, honesty ... Those are awesome properties and make her so nice. In the episode "AppleBuck Season" her stubborn unwillingness to allow friends to help her touched me, and since then I appreciate her.
Note: I love her rivalry with Rainbow Dash.
6. Rainbow Dash -My little pony: Friendship is magic: She is amazing. Initially she wasn't too sympathic to me because of her (little) arrogance, but now I love her so much and look forward to every episode and scenes with her. I don't know how this change came, but suddenly I like her (because she is a Pegasus, has a beautiful colors and her moves in the air are amazing, moreover I have interest to weather, clouds and sky, so I love the idea that pegasi control it), but the main reason is, because she wears a beautiful element -element of loyalty and I love the "loyal characters ".
7. Princess Celestia -First, she is very underrated character and receives a bad names for really bad reason. Second, she is very kind and forgiving and shows a real love and care to her subjects. And moreover, she's (was) a teacher of main character, Twilight Sparkle and they have a wonderful relation. I also adore the fact that she was a teacher even of Sunset Shimmer back when she was bad. And she acts like she's still able to forgive her, according to the first Equestria girls movie. She really has a lot of love and respect for others and she doesn't deserve all these bad names. She only tries to protect her subjects.
8. Princess Cadence
Another kind and sweet princess -princess of love. Again, I love her close relation with Twilight. I love her power and personality and everything. I don't care if she is a Mary-Sue. I love this kind of Sues.
Formerly my least favorite of Mane 6, but now she's pretty high in my list of favorite characters. That all thanks to season 4 and sort of Equestria girls. I finally saw her generous spirit and I was able to empathize with her. There were some episodes where I really loved her personality, so she grew to 9th place in my favorite characters list. And plus -she's visually the most beautiful pony.
Same reason as for Sunset Shimmer, even though he's much lower in list (maybe because of appearance? I don't really know). But I don't feel the same from him as from Sunset, since his reform took some time and he was able to betray even after reform and he wasn't fully reformed, so that's may be it. While Sunset was reformed immediately and she literally WANTED to redeem herself what makes her so valuable. Discord is a bit different case, but still valuable too, since he's reformed and this time probably totally.
The last 4 places aren't in exact order, I just love these characters so much that I can't choose between them.
I love more characters as well, but here I put only 10 which I think are the best for me.