I like how this plot is different than most Fluttershy episodes. It went towards to Fluttershy believing she is incompetence of flying fast and getting teased at for being useless, rather than OMG A BIG GIANT MONSTER IS HURTING/SCARING MY FRIENDS, I MUST DO SOMETHING. Every little thing counts, that's kinda of a good lesson. I like how Rainbow Dash tends to be there for Fluttershy and politely ask that she would attend the tornado event, usually I expect her to being a jerk about her slowness and refusal, but we know that's not what Rainbow Dash truly acts.
Nothing seems wrong with this episode. It was pretty straight-forward; no sudden Sonic Cuteboom from Fluttershy, her slightly speed boost was all needed to get the job done. Kinda wish we see that yellow-mane muscle-bound pegasus more often. Spike should've shut his yap, his words seems to discourage Fluttershy rather than helping, but at least it wasn't intended, he just wanted to be honest about the whole thing.