A minor variation has a pretty interesting idea and follows through on it to some degree fairly well. If you just read the major arcs(Nightmare Moon and Discord) while discounting the rest of the story, it flows pretty wonderfully.
Unfortunately, those chapters in between feel woefully incomplete. With exception to Boast Busters, the story doesn't really have much of anything resembling episodes, but rather scenes. We get a scene of Diane and Twilight Sparkle deciding to research Pinkie Sense, but nothing leading up to or following it. We get mention that Applejack is going to be leaving on occasion(it spawns the Mundane Made Awesome
item of the story page), but nothing really comes of it.
Overall, the story can suffer from telling and not showing, condensing plots that should logically have happened differently as barely different, if at all, from what happened from the show. Until you get into the Discord Arc after the Grand Galloping Gala(which is probably hit the worst with an In Media Res start and disjointed narrative), it feels like the author got bored with his own idea or even that someone else was writing it.