By the same token, have you had any issues with analog sticks? I haven't. I mean, I like the circle pad and understand why it was used in the 3DS but analog sticks have served me well.
As for the analog stick above the face buttons, I don't see a problem with it. Games that I typically play, either use the right analog stick occasionally for camera controls or heavily with the shoulder buttons. That said, I'm either using mainly the face buttons or mainly the analog stick so it doesn't matter to me where it's located. Being directly aligned is the only thing that would feel kind of awkward.