Before I vote, I'ma think about it while I write
Twilight is the main character of the show so she's got that going for her. She is magical, strong, a character that in my opinion we can relate to one way or another, she worries about unimportant details and makes a fuss over everything. The only reason I think she is not the best pony is because, lately in the series, she hasn't had many good episodes to show her personality... They are mostly about her adjusting to her wings or being a mary-sue (however you write that).
Applejack is, indeed, my fav. of the mane 6, but she is not the best of all of them. AJ is the only one I struggle to differenciate between them because, even though she is honest and hard-working, there is not a very outstanding feature about her IMO. But, she is indeed a role-model for people over the world for being so motherly, confident and always there for others...
Fluttershy is the shy lil' gal that everypony loves For good reasons. She is shy, dependent, cute (like, really cute), caring and very apologetic. But she has learned to stand up for herself (sometimes) and to not be afraid of crowds (again, sometimes). She is super relatable and I think she is one of the best candidates for the best pony because I can't find a reason to "dislike" her so...
Pinkie Pie is the pony that has been part of our happiness in our lives (i think). She parties, she's always happy (when i say always i mean 95% of the time), her motivation for life is to make others smile. With so many good things, there's something a lot of people dislike about her... She can be annoying (and as some say, out of character, even though I disagree). So... yeah... Sorry, Pinkie.
Rarity is the most surprising character of MLP in my opinion. She is elegant, pretty and generous. Usually the character I dislike in series, she surprised me by standing up for herself and being all around awesome I also can't find a good reason to dislike her character either so... Yeah possibly she's the best one.
Rainbow Dash is the great tomboy rainbow pony we adore (seriously some people love her so much it looks like they worship her...) Before I continue, she is not going to be my voted candidate simply because I hate people who aren't modest... I don't hate RD but I can't vote for her because of that fact. Anyway, she is cool, interesting and probably the character I am most like from the show. But, as I said before, I just can't bring myself to do that...
So, now it comes down to which one I like most... And my fav. between Fluttershy and Rarity is... >RARITY<