Guess it depends on what is meant by "better". They both have certain qualities about them that I think are great! But overall I think that Fluttershy is a better defined character than Twilight Sparkle. Twilight certainly isn't a boring character either though.

i can't choose them both are awesome! twilight is always reading and flutter shy is always shy

No way ::

Twilight is my number 1 and Fluttershy is number 2.

I like Twilight way better.

Twilight Sparkle always does whatever Celestia tells her to.. I mean, she cried when Celestia told her she failed. She doesn't cry when she's about to lose a friend or something..