For me, Fluttershy is probably the most complex pony and an courageous one at that. She is fully aware of all her flaws and accepts them (proof is when Discord is trying to corrupt Fluttershy in Return of Harmony). Since Fluttershy is almost afraid of everything (even just going to the market), and faces them everyday. "Courage is not a lack of fears, but the will to face them". oh yeah and she's SUPER adorable too!