Pinkie Pie's too divisive to be most popular. There's a core contingency who rate Pinkie Pie #1, but among those who don't rank Pinkie Pie #1, she's generally among the bottom-ranking members of the mane cast. I suppose she's wacky and has a unique sense of humor, and you either 'get' her or you 'don't.'
Twilight actually has the exact opposite problem. Everyone likes her, because there's so little to her that's offensive. But because the's the main character and often plays a straight and narrow role in interactions, she tends not to be the character that anyone loves most.
So in the "Save My" contest, for example, Twilight almost never gets anyone's first votes (everyone always prefers another pony more) but she'll always make a huge late surge once everyone can vote again, because she's usually everyone's "2nd favorite" of the remaining mane characters. Pinkie on the other hand almost always starts off very strong when her core pushes her to victory, but then her support drops off the face of the Earth, because almost no one views her as their "2nd favorite" pony.
...And Fluttershy typically dominates throughout because she is by far the most popular, and she also benefits from a personality that very, very few fans rank outside their top two or three. When it's down to only two or three mane characters, everyone who supported the mane characters that were eliminated usually rallies around Fluttershy. No one holds a grudge against her if she eliminates their favorite character, because she's adorable.
First time it was Fluttershy > Rainbow Dash and second time it was Fluttershy > Spike in the finals, so at least we'll get a new final match this time.
...I have run far too many of those contests to have microanalyzed them so much.
Edit: The two biggest differences I've noticed between B8's MLP fanbase and others: Rarity is more popular here than the norm, while Spike is less popular here than the norm.
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