Oh, man, where to begin...
The Cutie Pox - Easily one of the worst CMC episodes ever, and in my opinion, it's the worst episode of season 2. I still can't believe AKR wrote this.
Mysterious Mare-Do-Well - This episode has been thoroughly ripped to shreds by the fandom so there isn't much I could add, but it just amazes me how almost nothing about this episode makes any sense. This story honestly seems more suited for the comics.
Spike at Your Service - Spike has gotten some pretty bad episodes, but this has got to be the worst of the worst. It paints him as mind-numbingly incompetent and unable to complete simple tasks, which is virtually the opposite of his character.
Twilight's Kingdom - Outside of the scene that everyone adores so much, the writing here is just abysmal. This two-parter features Celestia at her most incompetent, and it's honestly to the point where I legitimately wonder why anyone trusts her to rule the country anymore. Twilight's decision to give up her magic was nothing but pure idiocy on her part, and in all seriousness, it should have gotten her and her friends all killed. There's definitely a problem when the plot is so heavily on your side that you cannot fail, no matter how dumb your decisions are.
Princess Spike - Almost as bad as SAYS, and definitely Spike's second worst episode.
The One Where Pinkie Knows - This episode was just annoying. It's one and only joke stopped being funny only five minutes in, and it was just painful that they kept it going to almost the final minute of the episode.
Newbie Dash - After FIVE seasons of buildup to this moment, Dash most certainly deserved better than this atrocity. Why they gave this one to a new writer will always be a mystery to me.
Flutter Brutter - Despite Fluttershy's excellent characterization here, Zephyr makes this episode borderline unwatchable. Definitely one of the worst characters ever introduced on the show.
The Cart Before the Ponies - I cannot even begin to understand why this episode exists. It's so out of place in season 6 that even if it had aired in season 1, Applejack, Dash, and Rarity would still have seemed out of character. It also did absolutely nothing for the CMC's new arc, thus rendering it all the more pointless. This episode could have easily gone towards advancing their arc, or even Starlight's arc.
28 Pranks Later - This episode clearly thinks that its dumb and pointless zombie gimmick would save it from its terrible writing and how OOC Dash was. It didn't. Yet another episode that could have easily gone to advancing Starlight or the CMC. Nothing of value would have been lost if this episode did not exist.