I almost went for Apple Bloom, since I think she's the most adorable of the trio and I can truly sympathize with her hard desire to earn her cutie mark. Buuuuuut, I kind of like Sweetie Belle a little bit more, mainly because of her reoccurring voice-crack, which is honest-to-Celestia one of the cutest sounds ever. I dunno, maybe for me, it's just a tie between AB and SB. As for Scootaloo, I haven't seen much of her yet (since I still haven't seen every episode as of right now), so I need to watch more of her to obtain an honest opinion.
I'd probably say Apple Bloom. I especially like her relationship with Applejack. I'm terrible at thinking of details, but it pretty much speaks for itself.
Scootaloo just because she's like a mini Rainbow Dash and Rainbow Dash is my favorite Mane Six member.
Apple Bloom was the second character I took a liking to. I really when her and Applejack work and play together. I think the only reason Scootaloo wouldn't be my favorite is because of all the weird chicken references I've seen and heard on youtube.