Well the last was actually addressed in a (admittedly dull) episode that to it's credit actually stuck. Fluttershy has never really hesitated to call ponies on their bullshit ever since learning that dealing with the Breezies.
I like Fluttershy's arrogance more than anything. The Applejack rivaling stubbornness in her point of view shown in the Kirin episode, or that near suicidal determination in "Health of Information". Hell even the slight bitchiness when defied is wonderful to see, as it turns her from caricature to actual person (most recently featured in "She Talks to Angel", where she comes across as surprisingly unreasonable at times).
And yes, she's surprisingly uneducated about animals sometimes, which is reasonably consistent but has never been specifically highlighted as such. I doubt she's had any actual formal training.
I do like Fluttershy in part because she is cool, competent and a nice person, but her flaws help frame that. Without that, she's admittedly flat.