Rarity is just the most consistently funny as well as the most flawed character. She's even more neurotic than Twilight, and neuroticism is the most funny quality they play off of in this show. Her VA also really sells her character perfectly. That's pretty much all there is to it. Rarity is hilarious and anyone who disagrees doesn't see eye to eye with me on humor.
Fluttershy and Twilight just tend to be pretty hilarious as well and are virtually tied at 2 and 3 for me. Rainbow Dash has her moments. Applejack is boring and remains boring, although when they try to make her not boring sometimes they succeed. Pinkie Pie's gimmick actually started to grate on me horribly this season, and I've grown tired of her. She was perfect in Party of One but she's become completely one-note ever since and that one note is irritatingly screechy.
Of course, everyone has their own opinions, but I've found that mine have pretty much crystallized this season and I'm a bit surprised not many people share my feelings.