So, just got back from seeing Captain America: Civil War. And it was amazing. I remember reading Marvel's original Civil War event. It was one of the first major comic events I read (having just got into comics) and ... yeah, it wasn't that good. Kinda the opposite. Partly because the pro-Registration side was, as Linkara observed, demonized throughout the series and most of the tie-ins, and in the end they were the winners and--according to remarks by the writers--were meant to be the right side all along! Even leaving aside the fact that the Superhuman Registration stuff was undone later. So yeah, Marvel can take a crappy comic and turn it into a great movie while DC can take several great comics and turn them into a crappy movie (and I say this as someone who generally prefers DC to Marvel).
What's the relevance to MLP? Well, it got me thinking: a big part of MLP episodes is that they often have messages or morals. Which isn't a bad thing, in and of itself. True, sometimes it makes things a bit formulaic and the plots easily predictable. Again, that doesn't make for a bad episode or a bad series. Heck, I got into My Little Pony in the summer of 2011 and I've been hooked ever since. It's the only show I watch on TV and I am head over heels in love with it. That doesn't mean I'm going to be pull any punches when I find an episode is lacking, quite the opposite, in fact.
Now, to tie my disparate thoughts together, most of the episodes of MLP that don't work (for me at least) tend to fail because of a failure of the moral. This can take several forms. Sometimes they present a moral or lesson that is at odds with what was shown throughout the episode. Say, by having the characters who are supposed to be in the right, the ones teaching the lesson, act so unlikeable that it deprives them of their moral high ground. Sometimes the different messages they're trying to convey trip over each other and become a mess. Sometimes the moral itself really isn't a good one, or requires more nuance than they were able to get across. Sometimes ... it just makes no flipping sense.
So I put it to you, the readers. What do you think were the biggest moral misfires (as I like to call them) in MLP? Can be any season, old or new. What moral/lesson episodes failed to get their message across? What morals worked, but were messed up in the execution? What morals themselves just didn't work? What episodes left you scratching your heads in confusion or slapping your faces in annoyance?