I think that Applejack is the least popular among fans because she hansn't done that much. That is not my opinion as I like Applejack. I have heard some stupid comments saying that Applejack's second episode (she's only had two) was more Derpy's episode which was silly. Derpy did not steal the episode, she appeared in one scene, that's it. I loved how Derpy was used, but she didn't steal the spotlight.

Rarity is underapreciated too.

I know who my favorire ponies are; Fluttershy and Rainbow Dash. Simply because I like them, I don't care how popular they are. I have absolutely no idea who is my third favorite pony and lower (even though I know the CMC also score high points - and even then I have no idea who the best CMC is) I still need to do my list of favorite ponies, and that's just FIM.