Usually with animated films, scenes are deleted at the animatic stage. That's usually the cheapest point in the production to decide to remove it. The film is still in a very incomplete state and potential plot/story problems are easily identifiable, and course corrections are easy to implement. So to see a complete deleted animated scene is a true delight.
Furthermore, the deleted scene is the original opening to the film! It's a prologue narrated by Twilight Sparkle and echos the opening to the entire My Little Pony: Friendship is Magic series. It does this by using an animation style which is complete different from the rest of the film, and the narration starts off with "In the magical land of Equestria." Though after watching the entire film, it's not hard to see why the scene was removed, since it straight up tells the audience what's going to happen in the film rather than letting them experience it as the film progresses.
There is one item to take note of about this scene. If you were at HASCON's My Little Pony Mane Event, you saw this scene in the movie footage shown there. I for one am ecstatic this scene didn't end up in the Hasbro animation vaults out for the world to see.
However, there is a problem. Namely that there is ONLY one deleted scene in the bonus features. If you were at Equestria LA and happened to be at the Making of My Little Pony: The Movie panel, you heard a ton of behind the scenes information about the film, including some alternate takes on a number of scenes and different story directions which were explored during production. And I'm pretty sure he mentioned a couple of times these were storyboarded and placed into animatics.
So… yeah. I just wish there were more deleted scenes to look at in this release.