In terms of fandom endearment, she's one of the most overrated ponies imo as her character arc post S1 has mostly been her relearning how not to be anxious and afraid of social communications in different ways while we have:
Twilight Sparkle: Learning to be a better friend that allowed her to become a new Alicorn Princess. She's right now undergoing an arc where she's pretty much trying to learn to be a leader for ponies, and being a mentor to the CMC's while trying to figure out for why the Cutie map wants them and is sending away missions for them to do.
Rainbow Dash: Learning to be less self absorbed of her abilities, becoming a wonderbolt, and being a loving surrogate sister and owner to Scootaloo and Tank respectively.
Rarity: Achieving her dream bit by bit to becoming a famed fashionista, learning to be more generous and to spread it for others to enjoy, and learned to be a more affectionate sister.
Pinkie Pie: Trying to bridge the gap between her family and Apples so she and Applejack can bond even more while learning to be more mature of her party planning and behavior.
Applejack: Learning to becoming the successor to Grannie Smith as matriach of the apple family and helping Pinkie Pie out to having their families bond with each other as cousins or so.
Sunset Shimmer: In 3 movies, she may have started off bad, but Sunset Shimmer has emerged as a more interesting character than Fluttershy imo as she became a successfully redeemed character whose arc in EQG series has emerged as one of the best attributes for it.
Fluttershy: The sad thing is that despite my criticism, Fluttershy is actually showing signs of development in S5 as they seem to be relying less on Flutttershy's anxiety to carry her (though I haven't seen the upcoming episode yet) in episodes where she's actually more assertive and she's not being so sheepish about it. However, if it weren't for her bond for Discord in S3 or so, she would literally have little to no development in between S2 and S5 as she had very little in character department in S3 and S4 that doesn't repeat a lesson she already learned in a different format.
Fluttershy isn't a terrible character imo, but when you compare her to some of the other characters on the show, she's definitely one of the weakest developed characters on the show despite having one of the largest sub groups in the fandom. The reason for this is the following points:
A. Due to how many introverts are in the fandom, Fluttershy was the most visible pony for many to bond with.
B. Her shy, moe personality is easily one of the most attractive personalities for many fans to grow attached to to a character.
C. Her cute design and love for animals is another factor for many to be attracted.
I can see why so many would bond with Fluttershy and be fans of her as it's not to say I don't like her. It's just the critic in me views her as a character that has plenty to be fixed or added to be put up to speed with other characters on the show for development.