Early on: Rarity. Before her career (and personality as a result) expansion beyond Ponyville, it feels like she was given episodes that only cared about her negative aspects, with episodes like Dog and Pony Show taking the concept of being manipulative and trying to spin it as being any less despicable, or by showcasing how petty she is by placing her anywhere near S1-2 Applejack. It left me with a sense of her being generous as a way to over-compensate for just about everything else about her.
Overall: Rainbow Dash and Fluttershy. The limitations of their archetypes being on both ends of the confidence axis and not much else made for shallow characters early on, with episodes being centered around “Don’t be an asshole” and “Be more assertive” respectively. Mid-series they finally got an expanded take on their personalities, but those episodes still shows up all too often whenever a writer needs to grab the first arrogant or shy character around, often “resetting” them to earlier versions of themselves for convenience’s sake.
Later on: Pinkie Pie and Applejack. Pinkie has always been a divisive character that walked a difficult balance between being the comic relief which doesn’t rely on self-depreciating humor while also being relevant in any way to the plot. What helped tip the balance (at least for me) was that she had the “outsider’s perspective” archetype and had opportunities to be the one to come up with the wildcard idea nobody else thought about, best showcased in Swarm of the Century. She also had a clear lack of empathy, one of her main aspects to which she could improve upon and in turn have episodes written about. This balance held questionably well…. until Starlight arrived and concessions had to be made on the writing side as to… shall we say, “enhance” her role. Some of the most significant changes were to take said outsider’s perspective and lack of empathy from our pink fluffball, kick em up and notch and feed them to the new arrival without replacing what was taken. Once the need for new Pinkie episodes came, they gave her the scraps. Episode ideas and character archetypes so specific they required a character to be shaped around them, not the other way around like you’d usually go, essentially making her a wildcard only in the meta sense of the word. This is what led to her being simultaneously AWOL from the plot 90% of the time but also the main attraction in atrocities such as Secrets and Pies, The Maud Couple and the utter eldritch abomination of an episode that is Yakity-Sax. Remember how amazing she was in Best Gift Ever? This would not have been allowed to happen had it featured another specific character, I guarantee it.
As for good ol’Applejack… well, she’s been stuck in a vicious cycle of character regression since S2, after writers understood early on that they just couldn’t allow a character to literally claim that she didn’t need to learn something from an episode to be left standing unharmed. What we’re left with after six whole seasons of pure mental decay, both in terms of morality/wisdom and general IQ is just begging for G4 to end with her likely departure. Just put the poor girl down, guys…
Whew. Sure felt nice to let that out, kinda what I needed. Tried to keep the bashing to a minimum, but…. yeah. Ain’t like it’ll even matter to some.