So arent those stats alone a huge red flag that something needs to be done, and quickly?
Contrary to popular belief, Riot doesn't just fire nerfs and buffs because of pick and win rate.
Thresh is going to remain a high priority pick regardless of how much you gut his skills- the W is THE GAMECHANGING ABILITY of League of Legends.
Anyone, any single champion, regardless of mana, health, cooldowns, summoners, can be pulled from a bad situation.
Does Thresh do other things? Yeah- but the W alone means his pick rate is assured to stay high. Nobody else has such a get-out-of-jail free card with an equal range and cooldown. They could straight-up remove the shield and it would barely effect the ability except it would be maxed dead-last. He's also ranged, which means he can bully tanky supports if they don't go in and bust him.
A high win and pick rate doesn't mean the champion is broken. Thresh has counterplay available for every ability active- he is a "fair" champion.
If he lands the Q, jumps to you, and E's you towards the carry while ulting- that's literally just as fair as any combo kit. They all have an ability that locks you down so they can use the rest of it on you.
However, a few things that might make him less dominant:
-
Range. Thresh's Q and W allow him to influence a fight from an extreme distance, have these scale slightly with rank, level, souls, anything- just enough to give him a bit of a nerf early on. Maybe you could even make his AA range grow with ranks in E but subsequently reduce it slightly at earlier levels?
-
Squishyness. Currently Thresh is strong because Support items just keep improving. If enemy laners aren't able/willing to bully him off of the souls- he will rapidly grow beyond their control since he will buy tank items and negate his main weakness of being squishy. A slight rate in how quickly the souls spawn would be another slight nerf to keep his early game down since he gains armor from them- which directly helps against the enemy ADC.
-
Harass. A slight tap to his total HP, HP growth per level, or HP regen could make any poke he takes a bit more potent, ensuring he has to either make his play or try harder to avoid damage.
Again, I don't think he needs nerfs, I think he's not unhealthy and, dare I say it, fairly balanced. The winrate isn't only reflective of his kit, but also the playerbase, the items, and all of those same things for his opposing supports.
Also, something I think that's seldom addressed is what I would call, "Experience creep".
There are many champions who are reliant on skilled play to make the best use of them. But the longer the game goes on (the actual game, the higher the percentage of the playerbase with enough experience and skill to make those plays will rise.
Thresh is fairly old, the playerbase has been learning his tricks for years now, skill floors can only hold you back for so long; eventually people will just get better at playing him.