Lee sin is unfortunately a ton of fun to play. I say unfortunately, because his kit inherently causes you to feel like you made a big play. While really it's just a more flashy version of the same thing. He is also just nonrestrictive in movement or resources, which is frustraiting if you ever run into the issue while jungling.
Also his early game is still incredibly strong, the natural power of his kit consisting of 6 high utility moves at level 3 still makes him feel like he starts out strong, rather than needing to get ahead through farm or fighting. What riot calls snowballing and almost treats as some negative aspect of the game. You don't want champions to snowball easily, but you do want them to snowball.
Lee sin's win rate compared to his pick rate is most likely a result of those two factors. People play him, go 6/0/3 in the first 20 minutes, then complain that their team is throwing the game for them, when really they were just piggybacking off of the innate power of lee sin's early game. Also his abilities just feel more flashy than most other champions, multiple dashes, a knock back, tons of combo potential, but that doesn't mean much in terms of actual power or effectiveness.
Riot always wants their game to be more flashy, but you can't assume that a flashy play will be a "good" play. It's just very easy to identify and clearly has some kind of effect. A lee sin, R is no more powerful than a
ult, but it looks like it has a much larger effect, because you literally sent the enemy flying and into their teammates.