You could easily balance Lee Sin in the early game and the late game by changing one small thing...

Make his E deal physical damage and nerf his Q. My god, it's not hard to do.

He's not balanced in the early game AND in the late game because of these scalings. Early game you can one shot someone because they don't have armor or magic resist, therefore putting the two abilities' damage together would be the same as if they were both the same type of damage. If his E deals physical damage, Lee Sin can not only just farm for the first few levels, not one shot a champion with any counterplay, he also wouldn't have such a terrible late game when he's currently forced to have over 8 kills before the enemy team decides to surrender.