CC counters everybody, but 1 cc can get master yi dead, and you need the entire team's cc to hopefully kill this monk.
When they design champs, they will lay out their strengths and weaknesses, so players can figure out how to exploit the weakness and avoid their strength. Lee's weakness is not tangible as it's Time, meaning his late game.
Let's not mention his late game is not a completely fallout like Shaco's if he doesn't get an early snowballing, he simply retreat and become a cc tank.
Also because of Lee standing out too much, he completely dominated jungle for 3 years. Riot, because of their poor management skill failed to realise why is Lee so strong and created a series of jungler trying to combat Lee Sin, before they come to realise that Lee is too good because he has everything.
Now they are currently in the position that they actually can not nerf him because once they do, the ones that were originally created to counter Lee will just rise and replace him become the new jungle cancer. Therefore instead of nerfing him they just keep this guy afloat, hopeing people get used to him rather than facing a new threat.
Tragic story really.
(Also the enormous Lee main outcry when they actually tried to nerf him, but let's not go there)