A few commenters on EqD voiced the opinion that Applejack was a poor character for creating conflict. I have to agree here. Irrational types like RD, Pinkie and Twilight are excellent for these purposes, and ambitious types like Rarity, RD(again) and Twi(again) are good for this too. Not Applejack or Fluttershy. Speaking of AJ,though, I think she'd prove more interesting when dealing with antagonists like the Flim Flam Bros. Her stubbornness and pride could work against her when dealing with business rivals, not to mention she has everything she ever wanted. Threatening what matters to her would be equivalent to threating the others' ambitions. Otherwise, she's a top-notch support character.

I honestly have little to say for Fluttershy, though. I never see stories about her, and it's been 12 episodes across two seasons since she's been a focus character (Magic Duel doesn't count, she was just being cute for the camera). AJ gets her next turn in two weeks with Spike, and Twilight's got that 'destiny' arc going for her (I pray to all the gods of nature and the sun and the heavens that she doesn't become an alicorn). She's just not that compelling in all honesty. AJ's a challenge in this regard admittedly, but Fluttershy seems hopeless to me in her canon state. I blame flanderization.