I would honestly be surprised if this didn't happen in season 5:
First, a recap.
Fluttershy has done the following things before:
gotten bullied by pegasi.
Tried to get Twilight to favor her over the others in "The Best Night Ever."
Hid her Vampirism( being a vampire bat.) from her friends to this day.
Befriended Discord (of all creatures.)
Chose Discord over her friends.
was double crossed by Rainbow Dash in "Trade Ya!"
During preview, Tried to bail on The group and stay with a currently sleeping Spike. (to no avail)
Did I miss anything? No? Good!
Now then, my prediction is Fluttershy will betray the mane "5" and try to eliminate Cloudsdale, thus removing all pegasi wings since they have no more use.