I can name a few more on my mind.
Twilight being shoehorned in season one. I don't think anyone will disagree on this. She was inserted in many episodes where she had no reason for it aside from writing the friendship report to Celestia. Look Before You Sleep, A Bird in the Hoof, Stare Master, Green Isn't Your Color, and The Show Stoppers all come to mind. (MrEnter accused Fall Weather Friends of shoehorning Twilight, although here, her inclusion is much more natural and settled more organically than the rest). But that was a season-one issue only. Following Lesson Zero, Twilight hasn't been shoehorned as much. Sisterhooves Social was the first FIM to not have Twilight involved, and it's easily one of the best in the show.
On the other hoof, since last season/late season two, we're now seeing the Mane Six in its entirety shoehorned too much, only worsening this season. Dragon Quest (Act 1 only), MMMystery on the Friendship Express, A Canterlot Wedding (although their roles were important, the Sidekick Five were pushed to the background), The Crystal Empire (same thing), Spike at Your Service (shoehorning Fluttershy and Pinkie Pie characters unnecessarily), Daring Don't, Rainbow Falls, Simple Ways, and It Ain't Easy Being Breezies. It's debatable if the Mane Six were shoehorned in Wonderbolts Academy, as Dash and Pinkie were the only ones with a purpose, yet had a reason to go. One important thing season two did right wasn't shoehorn every single character all the time; if they were there, it was for a reason. AJ, AB, Rarity, SB in Sisterhooves Social. Pinkie and Cranky in AFiD (the others as cameos). Rarity, Pinkie, and Fluttershy in Putting Your Hoof Down. Dash, Fluttershy, Twilight, and Spike in Hurricane Fluttershy. Rarity, Dash, and Twilight in Dragon Quest (the others cameos). While not all did it right, the fact that S2 didn't fall for the "shoehorn-the-M6" trap should be a factor to tell the team not to plug in every single character lest it's mandatory.
Several stories didn't need the moral to be shoehorned. Bridle Gossip, Over a Barrel, The Cutie Mark Chronicles (then again, the story called this out, but it doesn't mean I'll give it a pass), Bats!, Castle Mane-ia, A Canterlot Wedding ("trusting your instincts" is valuable, but has no place to be uttered by Celly in the last minute), Spike at Your Service, Rainbow Falls (although Dash learned it herself, it was so clunky by how blunt it was), and Mare-Do-Well really shoved the morals in unnecessarily or too bluntly to a character who was too dumb to figure it out. If your episode didn't need a moral spelled out, leave it out. Otherwise, show, don't tell. This is one thing season three did decently in. Magic Duel, Sleepless in Ponyville, Wonderbolts Academy, and Just for Sidekicks didn't spell out the morals via a report or journal. They figured it out and sometimes let us, the viewer, decipher it. But the one-shot to handle this the best was Pinkie Pride: It's also one of Maud Pie's strengths: The moral wasn't spelled out so bluntly nor reiterated in the journal. It was said once at the end, and that was it. (That said, the execution of said moral is another question, as the morals itself lacked focus, but that's another issue.) If you ask me, the recited moral is no longer necessary, and it would be more interesting for the audience to figure it out themselves. By doing this, the writer trusts the audience into knowing what the lessons were.
As of this point, the Twilicorn hasn't been taken advantage of at all. When Magical Mystery Cure and Equestria Girls were released, Twilight's ascension was treated as the evolution of Friendship Is Magic. Instead, Twilight's ascension has played a very minimal role and sometimes pretended it doesn't exist. Yes, Twilight Time did reference it, but it came way too late. Personally, that should've swapped Flight to the Finish's place as the fifth episode this season. So far, she's been the "I'm-right" or "I-have-the-solution" median for several of the episodes despite not having any business being there. If you're thinking, "Well, they've done this before," that's the problem. It's happened too much, and Twilight is simply a role-player instead of a character. IAEBB used Twilight, who was a background pony that episode, as a blatant DEM. Currently, the writers behave like they have no clue what to do with her.
Far too many episodes skimp on Celestia's reasoning and background stories of the villain. Currently, the only two stories with the most told backgrounds are Nightmare Moon and Sombra. Discord's and Sunset's expositions were brief and told very little. From my revised review for Keep Calm and Flutter On: If you're going to have Celestia give a reason, make sure they're efficient and not shortened for time. It cheapens her character and makes her like an inept control freak.
Several characters are one-dimensional. Snips/Snails, Shining Armor, Cadance, Dash's bullies, the teenage dragons in Dragon Quest, the plothole ponies from the marketplace in Putting Your Hoof Down, DT/SS lately, Sombra, Flash Sentry, Jet Set, Upper Crust, Trenderhoof, and Sunset Shimmer are flat, one-note characters. If you're going to introduce a character, at least put in some effort to give them some dimension. Make them real. One-dimensionalizing a character makes them walking cardboard cutouts. They're not interesting and waste everyone's time. (Gilda is flat as well, but at least Morrow tried, and she's two-dimensional.)
For too often, when a character does really bad or stupid things, they don't get punished for it. When a character performs such a vulgar stunt, then she should suffer the equal amount of consequence followed by a resolution in response. Sometimes, the punishment (if there is any) doesn't fit the crime. To give you examples: a. Babs Seed from One Bad Apple. Already explained this. b. Rarity from Sweet & Elite. Here, Rarity decides to stay in Canterlot to attend the party over celebrating Twilight and her birthday party. To say the least, what she did was unbelievably cruel and didn't exactly have a good reason for it. S&E presented Rarity as very out of character. To make matters worse, when Rarity was confronted, she not only was forgiven, but was rewarded, and she was still able to keep her vile lies a secret. Just because she learned her lesson doesn't mean she shouldn't have been punished for it. Rarity should have been scolded, embarrassed, and shunned for her betrayal of trust. c. The Cutie Mark Crusaders for poisoning Cheerilee and Big Mac. They realized how badly they screwed up and wanted to fix it so badly. Hell, they felt very guilty for doing this. I can agree that making them do Mac's chores is sufficient, but Cheerilee and BM rubbed salt in the wound by acting like the love poison never went away. It was cruel, disgusting, and out of character of Big Mac (for a while, he went into my hated character list before I smartened up), Cheerille (same here, except I never liked her that much in the first place), and the show. d. Diamond Tiara and Silver Spoon for coercing Babs Seed to bully the Cutie Mark Crusaders and mocking Scootaloo's inability to fly. e. The Remane Five acting like hypocrites in TMMDW. If you want to get your point across, don't do the same thing and embarrass one of your closest friends behind her back. It was a disgusting act that NONE of the characters would ever do, and they were rewarded for their efforts. f. Stalkerjack driving Apple Bloom so crazy, she decided to deliver the pies herself. The fact that AB had to do this in order for AJ to realize she was babying Apple Bloom was insufficiently stupid. Instead of AJ suffering the consequences of her actions, Apple Bloom's the one who will. Idiocy to the core. g. Spitfire and Fleetfoot for being assholes and lying to both Soarin' and Rainbow Dash so she gets to be on the Cloudsdale team over him. They purposefully abandoned their closest teammate for no good, in-character reason. And what d'ya know it? It was all forgive and forget, and RF acted like it never happened. If you want Fleetfoot's and Spitfire's cruelty to hit, have them kicked out of the Cloudsdale team and replaced by other members, punished for violating the codes of the Wonderbolts, and have Soarin' temporarily end his friendship with them. h. Pinkie Pie in Filli Vanilli, Apple Bloom in Bridle Gossip (leaving AJ for dead in the Everfree Forest), every one of the Mane Six sans Rarity in Ponyville Confidential (being massive hypocrites by endorsing the gossiping before turning around after realizing they were the victims of it), the Mane Six in Games Ponies Play (being stupid and out of character, only to get rewarded for their efforts), and Philomena in A Bird in the Hoof. No effective consequences for their bad behavior. There needs to be more and more episodes where the characters suffer the consequences for their bad actions. If they do something bad and suffer the consequences, make sure it fits the crime and not to overdo it, or risk making it look abusive. Examples of such punishments that fit the crime: a. When the Remane Five trespassed the Castle of the Royal Sisters in Castle Mane-ia, they suffered from some darkly hilarious hijinks, including Fluttershy believing Angel was crushed by debris. Funny, yet disturbing. b. Rarity in Sisterhooves Social is one of my all-time favorites that follow this demonstration and is slowly climbing up on my all-time favorite list as a result. She didn't pay any attention to Sweetie Belle, lost her cool, berated Sweetie, and didn't want to spend any quality time with her. As a result, their relationship was fractured, and Sweetie was too hurt to easily forgive her. When Rarity tried to say sorry, Sweetie didn't simply forgive and forget because she hurt her and wanted it to stick. Therefore, Rarity had to team up with Applejack to rectify it. By disguising herself as Applejack, Rarity was able to team up with Sweetie Belle and come in second. They forgive and forget, and Rarity learns a valuable lesson. c. Because Suri took advantage of Rarity's generosity so vindictively, Rarity all but abandoned her biggest quality because she felt it made her look worthless and didn't want it to happen again. She got so involved into one-upping Suri in the Fashion Week contest, she didn't realize she took advantage of the Remane Five's effort. After realizing what she had done, she grew extremely upset and no longer cared about the show anymore. (God, that episode did SO much RIGHT! ) d. In Suited for Success, the Remane Five acted as clients within their respective personality perimeters, disregarding Rarity's sense for design in favor of what they wanted. In return, they got extremely embarrassed in front of Hoity Toity, and Rarity became a laughingstock. To remedy their misdeeds, they teamed up to complete Rarity's dress for the Grand Galloping Gala. e. After Lightning Dust continued to disregard anyone's lives except her own (including nearly killing Dash's friends), she got demoted and kicked out. Although the original ending had Dust realizing what she'd done and gave the episode closure, Dust's actions would've been considered to be okay and not worthy of an expulsion. By emphatically ripping the leader badge from her uniform, Spitfire made the consequences stick. It was the more satisfying conclusion. f. Applejack and Dash were at their (in-character) worst in Fall Weather Friends, trying to one-up each other and mocking Twilight for deciding to enter the Running of the Leaves. But by focusing on themselves, they didn't do what they were supposed to do, resulting in fighting and tying for last place. After their fight, they look like they got scraped badly, embarrassing themselves and realizing their big mistake. They learned a very hard lesson, and it worked deliciously well.