Canon Foreigner: The dragon doesn't appear to be any of the ones from the show.
Death Is a Slap on the Wrist: Dying in the platforming segments leaves all the items collected and walls destroyed. Dying in the boss fights causes the player to respawn instantly while the boss retains damage done, making extra lives work more like extra health bars.
Death Glare: Fluttershy's Stare has been powered up to the point where it can destroy stone walls.
Dual Boss: The Ursa Major and Ursa Minor in the second game.
Final Boss: Discord. His fireballs are really hard to avoid.
In the second game, the final boss is the Changelings, a pretty unrelenting Wolfpack Boss that is fairly hard (by this game's standards).
Fricking Laser Beams: Twilight and (surprisingly) Rarity both attack with those. In the second game, Fancy Pants and Shining Armor do the same. On the boss side of things, there's King Sombra and Trixie.
In the sequel, King Sombra and Trixie are this if you play as Shining Armor or Fancy Pants and the final battle is against a group of Changelings that mimic the player character's attacks.
Palette Swap: Gameplay-wise, Rarity is exactly the same as Twilight Sparkle. Somewhat glaring, since not only is she the only palette swap, the others at least use abilities resembling the ones that they have in the show. Still strange though, especially since Applejack or even Rainbow Dash's attacks would fit better since Rarity has usually been depicted fighting with her bare hooves on the show, using what might be some kind of pony martial arts.
Poor King Sombra has been relegated to this status in the second game. He is like Trixie without the teleport and the starting invincibility, which is a little jarring because in the cartoon proper he was actually a massive threat.