Fluttershy is so, SO strong. She's shy and timid and downright quiet at times, but her power is astounding when it comes to surface. I see quite a bit myself in her. Well, her and Rainbow Dash. I'm sorta caught right in between them, personality-wise. (I might have a hint of Pinkie Pie in me, too... I love to make people laugh and smile. )
Very well thought out and cogent, but the only point I disagree on is with Fluttershy's characterization in Putting Your Hoof Down. I enjoyed how it showed the vast dichotomy between Fluttershy when she is trying to live up to an unattainable standard (like what Iron Will set for her), and when she is being true to herself while still getting what needs to be done done (like what happened at the end of the episode). It helped develop Fluttershy a bit more as a character, and while she is still the kind sweet pony that we know and love, she can also stand firm in what she believes in.
I admit that the Fluttershy episodes have gotten a bit formulaic, but she seems like the type of pony that would need a refresher on what it means to be assertive and to stand up for yourself, lest she slip back into bad habits. I really enjoyed this essay, and I hope I can see more well thought out works from you to help bring some sanity to this raging fan base.