There aren't any episodes I can think of I hated, or even disliked really, though there are certain aspects I'm critical of in particular episodes. It's About Time: Eh, nothing to see here. We've already been through Twilight's obsessions, and I called what was going to happen as soon as Twilight ruined her mane. Cutie Pox: Filler. Meh. MMMMystery on the Friendship Express: While on one hand, I laughed pretty hard at certain points, again, nothing much happened. It's a whodunit episode, but that's it. And BOY was that moral at the end forced. Ponyville Confidential: When did Diamond Tiara's voice get so much deeper and louder, and why is RD dumping rain on a filly who idolizes her? Really, what's with the disproportionate amount of Rainbow Douche moments in season 2? A Canterlot Wedding: Didn't care much for how the relationship between Twilight and Shining Armor was portrayed. They went the "big brother best friend" route that made you wonder why in the holy heck this obviously new character hadn't been brought up before, and Twilight's overprotectiveness bordered on creepy. That said, I just disliked those aspects, not the whole episodes. I don't really agree with all the Gilda hate, to be honest. At least on some level she cares about Dash and tries to control herself a little around her. Though you can hardly fault Dash for saying, "All right, enough of this ****, either respect my new friends, or drop me as one."
I think the two episodes where the cutie mark crusaders where trying to get their cutie makes where my two least favorite.
Putting Your Hoof Down. The only episode I outright dislike. I didn't really like the time travel episode either. Too much happened for no apparently reason other than to stress out Twilight.
If I had to pick just one, I'd choose Mare-Do-Well as some others have. I just feel like the whole thing was a slap in Dash's face (which it literally was at one point) from all of her friends. Rather than have a nice sit-down talk with her, and explain that she was showboating too much, they had to devise a complicated plot to completely humiliate her in front of everypony in Ponyville. As much as I disliked ego-Dash in season two, even I thought they went way too overboard in trying to show her what she was doing wrong.
i dislike any episode with the CMCs in it, and the train mystyry one. i just find the cutie mark crusaders annoying, and as others have said, the train one kinda lacked plot. why so much hate for mare do well? maybe im just evil, but i kinda think rainbow deserved that slap in the face. you have to admit it, she can be pretty egotistic somtimes.
I really don't like the CMC, so any episode that's CMC centered I don't like. I also don't like Dragon Quest.