Fluttershy has wing hands in season 2.

She has a prehensile tail as shown in season 4, 5, and 6. (S04E07 as Flutterbat, S05E21 when she was hanging upside down while disguised as Flutterbat, and S06E18 when she can catch a buckball with her tail and send it back)

And now her mane can revert back to normal after pulling off a disguise. I would say that Fluttershy's character/personality isn't the only thing that has developed over the series.