At Canterlot Gardens, I had a brief conversation with a fellow running the EnterPlay booth in the merchandise room. He said he had to ask the essential question, who is the best pony? He had an interesting perspective, where the older/more entrenched the fan is, the more complicated the answer. My friend, who came to cosplay with me, gave a very concise answer. I responded with an abbreviated answer which I will reiterate and expand upon immediately.
The first and singularly most important notion to wrap your head around is that the question cannot simply be “who is best pony.” Above all else, one must categorize the characters in the show. With such a diverse cast, it makes absolutely no sense to generalize a multi-dimensional character as ‘best.’ For example, a series of good categories to select ‘best ponies’ from could be: Mane 6, immediate supporting pony characters, villains, nominal pony characters, nominal non-pony characters, pets, background pony characters, and background non-pony characters. Immediate supporting pony characters include (but are not limited to) the Apple Family, the CMC, and royalty. Nominal pony characters include (but are not limited to) Mayor Mare, the Cakes, Diamond Tiara, Silver Spoon, the Wonderbolts, Fancypants, Photo Finish, Hoity Toity, Sapphire Shores, and other featured speaking ponies. Villains include (b.a.n.l.t.) NMM, Discord, Chrysalis, the Diamond Dogs, Gilda, Trixie, Garble, and the Flim-Flam brothers. Nominal non-pony characters include (b.a.n.l.t) Steven Magnet, the various cooks on the Magic Express, Iron Will, Cranky Doodle Donkey, Zecora, Chief Thunderhooves, and the like.
Inanimate characters (Madame LeFlour, Tom et. al.) can also have their own category. Creatures (Manticore, Hydra, Cockatrice, Parasprites, Ursae, et. al.) can also have their own category, although it might overlap with the background non-pony category. Spike and Derpy can duke it out.
Fancharacters are totally separate, as are variations on real characters and headcanon/fanon. Sadistic Rarity and Handsy Lyra are not the same characters as the ones they’re based on. Do not confuse the two.
Secondly, one must adhere to a set of strict criteria which one will base their selection on. For me, AJ has the best element of harmony, Rarity is the most aesthetically pleasing of the Mane 6, but Twilight is my favorite. Why? She’s the main mane character, for one. For two, I identify very much with her. For three, she’s purple, and purple is the best color, not to mention it’s a non-spectral color, which are the coolest colors. The list continues. Pinkie Pie is an excellent character in general, and Fluttershy is indubitably cute. For me, RBD is honestly the least appealing character of the Mane 6.
Princess Celestia is my favorite royal figure. Discord and the Flim-Flam Brothers dual-head my favorite villain category. I haven’t given as much though to the others. If Pinkamena doesn’t count as a separate character, though, Pinkie Pie bumps up above AJ in my ranking (TS > R > AJ/PP > FS > RBD).
Thirdly, favorite character needs not coincide with favorite ship. For example, my favorite background character is tied between Dr. Whooves and DJ PON-3/Vinyl Scratch. However, my favorite background ship is between Lyra and Bonbon.