BEGINNING OF EACH SEASON= SOMETHING TO DO WITH ROYALTY
the two-parts episodes are centered around the very small storyline, which will always have something related to the royals. Celestia and Luna have to guard Equestria. these two-parts always have the BIG BAD GUY GONNA TAKE OVER EQUESTRIA, so they have to at least tell Twilight to go fix it for them
though i wish they'd get a bit more involved in the process