While it feels a little rushed in parts, especially when Fluttershy's "problem" comes to light, overall it's a fairly solid work with some cute scenes.
The plot itself is very much like an actual episode: AJ finds that her trees are being stripped bare of apples and destroyed, so Fluttershy is (eventually) called in to help. It starts off as a light friendship comedy, moving onto a parody of detective stories, before finishing with a fairly dark action-oriented climax. It didn't bother me too much, but it might be a little genre-shifty for some tastes.
I said in my comment on the fanfic rec that it had a nice Original Flavour. Some scenes really capture the zaniness of the show, like the wyvern chase scene and Fluttershy's attempts at detective work. There's also a touching scene near the end between Fluttershy and Applejack, and the overall friendship lesson is an appropriate one that could fit comfortably into the series.
Fluttershy's characterisation is very true to the show, even if the scene where her problem is revealed is unbelievably swift, almost to Mood Swinger
levels, while Applejack and Big Mac make a neat comedy duo. However, there are times when Applejack seems unnecessarily rude, and one scene has her be a little more patronising towards Fluttershy than she really would be in the show. But even so, she's still recognisably Applejack for most of the story.
The pace is pretty uneven in the middle, with a drawn-out part followed by a quickdraw scene, and that's the weakest aspect of this fic and one of the few things I'd fault it for.
Overall, though, I'd give it an 8 out of 10. It's still pretty fun to read, and what it lacks in technical detail, it makes up for with a lot of heart. And plenty of jokes!