It being misdirection would be a huge disservice to the character of Littlefinger. He's one of the three smartest men in Westeros,

Where are you getting that "three smartest men in Westeros" figure, I don't remember anybody in the books or show saying that but it would be easy to forget I suppose. Either way not sure I agree.

and he's supposed to be outsmarted by a psychologically damaged girl with basically no education?

Have you not been watching the Arya scenes of the last few seasons? She's been formally taught by the Faceless Men in addition to the lessons she undoubtedly picked up the likes of Sandor Clegane and Tywin Lannister.

People are just mad because they like Arya, and they don't want her to do bad things

No they're mad because she's saying and doing things that contradict her character development.

But her doing bad things is what makes her character interesting in the first place.

Agreed, for the most part, I just want the reasons behind those actions to be reasonably consistent.