A pony's special talent and cutie mark are determined through the name of the actual pony. The name of the pony magically embeds itself and magically determines the fate of the pony. The name chosen by the parents are also somewhat magically influenced as well. Otherwise ponies would name their children something to guarantee success like "Filthy Rich" all the time.
The magic mirror events in an alternate reality did happen but it was still with ponies instead of humans but there was no magic or unicorns or pegasi.
The Doctor is canon (see big mac comic from IDW)
Apple cider IS alchohalic.
Luna is never around during critical moments because she is too busy going to night clubs and other parties.
Fluttershy can't make animal friends at the gala because those animals are constantly harrassed by canterlot civillians.
Earth ponies hooves have magical fertilizing hooves that boost the growth of plants when they hold the seeds. This causes them to be more bountiful.
Celestia wanted to return her sister from the moon before 1000 years but did not have a spell that could return luna from the moon or was only magically capable of sending somebody to the moon and not back.
Prince Blueblood was adopted into the royal family.
Lyra is not obsessed with humans.