Fluttershy was originally an Earth Pony while Pinkie Pie was originally a pegasus. They switched it around due to the contrast it made; Pegasus Pony who is more down to earth while an Earth Pony has just about as much energy, maybe even more than, a regular Pegasus Pony.
Plus, Fluttershy and Pinkie Pie were originally going to be Posey and Surprise from the G1 Series, but due to copyright issues, they had to change it around.