Okay, here's the eps in my Discontinuity pile, along with reasons:
Mysterious Mare-do-Well - Because the level of technology present totally contradicts every other episode. In "Winter Wrap-Up" snow-ploughs had to be pushed by ponies manually, but this episode has a pony driving a tractor which seems no different than the kind us humans use (which should be impossible).
A Friend in Deed - My big problem is Pinkie's portrayal and how this episode feels more like its trying to advance her as a marketing icon than tell a story. That it introduces donkey homeowners is just the cherry on top.
Putting Your Hoof Down - Angel, who has always been shown as caring for Fluttershy, in this episode kicks her out of her own house for not putting a cherry on a damn treat. Ponyville is inexplicably dark and mean-spirited. Also I found Iron Will just obnoxious, and probably would have hated him even if he weren't a minotaur.
Dragon Quest - I actually
would have accepted the dragon society if they had behaved more exotically and not like a bunch of stereotypical white american male teenagers. On top of that... dragons want Spike to kill a baby (essentially), then act like they're gonna kill Spike. Again, way too dark for this particular show. The "namby-pamby pony princess" B.S. just seals the deal.
Mmmystery on the Friendship Express' - Return of face-of-the-franchise bland mascot Pinkie (as compared to the Pinkie who gave us "Forever!") who now talks like she's got problems (okay, so she kind of
does, but still). Also I know I'm in the minority but I
hate classic movie homages, especially since Twilight acknowledging a laser defense system without questioning what it is brings up the same technology issues that MMDW had (I tend to see homages as a sign that the writer ran out of ideas, too).
Really, its less "I'm speciesist" (though I totally am) and more "having a non-pony named character is the first sign the episode is gonna suck."