I love this thread, i always had in mind some anime characters related to the mane 6.
Fluttershy: Usagi Tsukino (Sailor Moon): both are cry babies but gold-hearted. Fluttershy, like Sailor Moon tries to make the enemy a friend (Fluttershy-Discord/Sailor Moon-Sailor Galaxia) instead of defeating it. They both know the real meaning of mercy and make us know that there are lots of other ways to solve things without using violence. What is more, Fluttershy's pet is a bunny, and Usagi in japanese means bunny too.
Twilight Sparkle: (and this is for you Bardock ) : Bulma Brief (DB) : Bulma is my favorite character of all time, love her! They both are very intelligent and pretty, they know what to say in the right time and always have an answer for everything.
Pinkie Pie: Lime (Saber Marionette J): They always laugh and they both are very optimistic characters.
Rarity: Mikami (Ghost Sweeper Mikami): Both are sexy and determined.
Applejack: Minako Aino (Sailor V/Venus from Sailor Moon): They look alike. Their personalities aren't the same but both are loyal friends and always want the best for them.
Rainbow Dash: Ranma female version (Ranma 1/2): Both have a tomboyish attitude but they have self-confidence.