Now don't misunderstand the title of this post, the good outweighs the bad and it's still one of my favorite shows, but no show is absolutely perfect, is it?
10: Sending Twilight away
Now, in-universe I understand why Applejack and the others sent Twilight away in Princess Twilight Sparkle, even though I do not know how they thought they were going to defeat the "villain" behind the Plunderseeds without her and they were feeling quite foolish once they got there. But out-of-universe, it was done just to fill the full 22 minutes of the episode. I think a flashback to King Sombra (between the Nightmare Moon and Discord flashbacks) would have been better, it would have pleased more fans by giving him more lines and screentime, as well as showing that just coz he's dead doesn't mean he can't reappear in the show.
9: The Cutie Mark Crusaders not realizing their special talents
Apple Bloom is good at construction and designing stuff. Sweetie Belle is an excellent singer, and Scootaloo is pro at riding a scooter. Their special talents are right in front of them and they can't see it (especially with Sweetie Belle's stage fright). I know this was played for comedy but still. (although there is speculation that they get their cutie marks this season)
8: Cheerilee being oblivious to Diamond Tiara
Though quite a good-natured teacher, I still find it irksome that when Diamond Tiara passes the note to Apple Bloom, only Apple Bloom gets caught, and she completely ignores Diamond Tiara making fun of Apple Bloom for being a blank flank. (Diamond Tiara herself would have a spot on this list if she didn't always get comeuppance each episode)
7: Doing the Indiana Jones reference wrong
Two classic Indiana Jones scenes are Indy going under a sliding door and pulling his hat through at the last second (Temple of Doom) and him switching the artifact with something else (Raiders of the Lost Ark). However, Daring Do, the Indiana Jones pony, does both of them wrong. The hat thing isn't done when she goes under the door and she doesn't switch the Sapphire Statue with anything. Every other show that has done this reference has done it right, why not MLP? (atleast they did a decent version of the Word of God challenge, and the "red line on the map while travelling" thing with an entertaining twist, is The Last Crusade the only movie the episode's writer has actually seen?)
6: The Plunderseeds
After waiting so long for Season 4 I was expecting a new villain - one on a Chrysalis scale at least. With screentime, lines, and character. Instead we got these black vines created by Discord before he was turned to stone, which were suppressed by the Tree of Harmony's magic until the magic disappeared for reasons unknown (it survived a thousand years without the Elements).
I had two explanations for this: The first was that they were unable to come up with a new villain, or lost confidence after the Sombra thing. However, in the season finale, Tirek was everything I was hoping for (with one minor exception but I don't need to get into that) so I figured that they had their heart set on him for the epic conclusion to the Keys of Friendship arc and the only way to keep the gender pattern consistent (villains have always alternated between being male and female) was to have no villainous character in Princess Twilight Sparkle, instead being minions of a currently reformed villain. However, Starlight Glimmer coming right after the Dazzlings breaks the gender pattern, which I guess was just a coincidence.
So, I think they were just being lazy, because I think saying some villain besides Discord was behind the Plunderseeds would have been better. Sure, he/she would probably be destroyed along with the Plunderseeds much to the rage of many fans, but I still think the survival of Tirek and the Dazzlings (and the freedom of the latter despite their de-powerment) should atleast give them satisfaction since they're everything people liked in Chrysalis minus her unexpectedness.
5: Pinkie Pie being insensitive to Rainbow Dash
Pinkie Pie is my second favorite pony but there was one time I disliked her: In The Super Speedy Cider Squeezy 6000, where she gets like 50 mugs of cider so Rainbow Dash doesn't get any, and then twists the knife by describing the whole cider drinking in front of Rainbow Dash. That was just cruel. (sometimes I think Rarity put her up to it after The Last Roundup) However she does redeem herself in the end by giving Dashie a mug of cider
4: Twilight, Rainbow Dash, and Rarity not fighting the teenage dragons
Twilight, Rainbow, and Rarity looked like they were ready to fight Garble and his gang. If not kill them, at least give them a beating and leave them humiliated at being defeated by the "namby pamby" ponies that they were making fun of, even though they did kinda get a lesser version of that. However, instead the three ponies just ran away when they could have taken them.
3: Manehattan ponies treating Princess Twilight rudely
In Rarity Takes Manehattan, when Twilight asks the ponies to let Rarity take the cab, they rudely respond "Not likely! She can get in line like the rest of us!" I know it sets the stage for one of the taxi ponies returning Rarity's generosity, but Twilight Sparkle is a princess. Would they talk to Celestia like that or did they not see her wings and horn?
2: Equestria Games
They'd been building up to the games for as long as the Keys of Friendship arc. And the Equestria Games episode came right before the Tirek episodes that conclude the Keys of Friendship arc. You expect them to show the Equestria Games, you expect it to be almost as big as the Tirek episodes. However, instead we get a Spike episode that basically recycles the plot of Sonic Rainboom and Hurricane Fluttershy.
Also the fact that they disabled the princesses' magic along with the other unicorns. If they had their heart set on the Spike thing, they could have a.) Balanced him with the games, and b.) given some indication that the princesses retained their magic and were ready to do something, but Spike gets there first, showing he is even quicker to act than the princesses in this situation, which would have even more power when you think about it.
It is ironic that my least favorite episode and my favorite episode (counting Parts 1 and 2 as one) are back to back. It is also ironic that my least favorite episode is also the only one that all three of my favorite characters (Rainbow Dash, Luna, and Gustave) appear in, but Gustave is hard to notice and he and Luna do not speak.
And the number one thing in this show that annoys me the most...
Warning: This relates to one of my two favorite elements in any show, which many people do not like me to talk about. Anyone who knows what those two interests are and hates to hear me talk about it, leave. You have the power to walk away without reading it. If I hear enough negative comments I will remove it.
1: The Hair Extensions of the Anthro forms
When the human ponies turn into their Anthro forms in Equestria Girls, despite gaining actual pony ears and, in the case of Twilight, Rainbow Dash, and Fluttershy, actual wings, instead of actual tails they get hair extensions that look like the tails.
This wouldn't be nearly as big a deal if My Little Pony: Friendship is Magic wasn't the one show where characters do the most things with their tails, including the video game trilogy Gex at its minimum (yeah, I took count) and excluding Pokemon with its 850+ episodes (though atleast the dub ended in May, albeit by cancellation), so it should be the last show you'd expect to walk away from that. Instead, that subtheme is diminishing just like it did in the show that gave me my interest in tails (namely Dragonball Z).
As Rainbow Dash, Applejack, and Sunset Shimmer refer to them as tails, as do the books, I think it actually was supposed to be tails, but either the animator or the one who designed their toys (whichever came first) messed it up. Also, when Sunset Shimmer turns into a demon, she does have an actual tail, implying that they think tails are a demon thing. (usually horns are associated with demons first but Demon Sunset doesn't even have a horn, even though she is a unicorn, which also begs the question why don't Twilight and Rarity get unicorn horns either? Also, Satan isn't the only creature that has a tail - most animals do too, including, you know, ponies!) And before you mention her phoenix form, that was more of a metaphor, she didn't actually take that form.
Though if you want out-of-universe things, hiatus tops even this on the list which is why I want the show to end already so we don't have to wait for more. Although if any of you want to do a similar list, I can imagine Flash Sentry would be pretty high on many of them