Applejack and Rarity were both being petty as hell, and Rarity did cause as much conflict.  Also, Applejack's point was that if Rarity had actually taken off the branches like she was supposed to, then the tree wouldn't have been so large and heavy on the top to have become so unstable when struck by lightning. 

Also, I don't get how you defend Rainbow for her flaws (Yes, I did see your defense of Rainbow Dash), saying it's part of who she is, when you criticize Applejack for flaws which are also part of her character.  And Rainbow is much more flawed than Applejack, being an outright jerk to others and constantly boasting, while Applejack is mostly just stubborn.  And you said this person criticizing Rainbow for mocking Twilight must be an Applejack fan, which first of all, is an assumption, and second, at least AJ didn't cheat until after Rainbow was repeatedly cheating in their competition for a long time.

At the time you wrote this, Applejack was very underdeveloped, meaning she didn't even have many flaws beyond simple stubbornness...which is kinda the same now. 

And this is coming from someone who doesn't even like her all that much.