It's not always a good sign when a cult television show cuts a season short to make time for a feature film. Case in point, my all-time favorite show Mystery Science Theater 3000 did it in 1996; they'd produced 24 episodes a year since 1991, but for their seventh season they only made six episodes to make room in their schedule for Mystery Science Theater 3000: The Movie. I don't dislike the MST3k movie at all -- I saw it more than once in the theater, and ask me sometime to show you my collection of promo merchandise -- but all things being equal, I would have preferred more episodes.
Similarly, the third season of My Little Pony: Friendship Is Magic was cut down from 26 episodes to 13, most likely in order to make the feature film My Little Pony: Equestria Girls. And while the movie (which hits video today) is not without its charms, in the long run, I'm not convinced it's a good substitute for a full third season.