my theory is that seasons 1 through 3 all took place in one year, and the episodes within that year are all in a jumble, while season 4 is mostly chronological and takes place over the course of a few months. why is because the only festival that has ever repeated itself in the show is the summer sun celebration, and the times it happens in the beginning of seasons 1 and 4. also, at the end of "the show stoppers" scootaloo hugs rainbow dash even though it isn't until "sleepless in ponyville" that she becomes dash's honorary sister, which means that "the show stoppers" happens after "sleepless in ponyville.
that's all i have so far . the rest is still just a jumble.