The writers really needed to drop the S1 formula that required Twilight to write a friendship letter and effectively obligated her presence in every episode. Stare Master was negatively impacted by the old formula, bearing in mind that it had a handful of other problems.>>36827816
Or maybe for The Cart Before the Ponies, the episode would have been better off starting with the race, leaving the musical number and all intact, then after the wreck, the fillies forfeit the race, frustrated at their older sisters for having taken advantage of them. Then throw in a second plot device while the whole episode focuses on Applejack, Rarity, and Rainbow Dash trying to make it up to them for being such terrible siblings. That way you get more screentime on the likeable side of the Mane 6 while still leaving their character flaws (if you consider their bad side "in-character") part of the story.
The three older siblings came off as unlikable in the story, but that wasn't particularly my main gripe with the storywriting. My main gripe with that episode was its story structure being all over the place.
If I were to choose to alter an episode, I would rewrite "The Times they are a Changeling" and drop the musical number, let Thorax be arrested, and have spike help him break out of jail and deny involvement to anybody except for Starlight, who then might have foreknowledge of the changeling invasion for the season finale.