I feel a lot of these cases was purely because it was the first 3D Mario. You can't have the same expectation for all of them as the magic of experiencing that again for the first time is gone. I've still enjoyed subsequent Mario games, sunshine was probably my favourite. But then again, the GameCube is my favourite console of all time.
I am not a Zelda fan or a Mario fan, but Twilight Princess was my favorite Zelda also. I cannot stand Ocarina of Time or Majora's Mask, they just don't hold up well to me. And that dumb fairy in OoT always screaming at you.
They definitely set the standard. The mechanics aged well, since they're still using them.