Yeah i understand what you're saying. But that's true of every defender. There is no perfect defender. Maybe the problem was talking in superlatives (the best x) rather than talking about quality because the moment we do that, the reaction is to point out flaws that make a defender less than perfect. Which is the case with everyone.
Long route or hoof football is easier to deal with for a big defender,as you said, but that isn't the only good thing he's at, in my opinion.
He reads the game well. Little things that we don't usually focus too much on. When a striker has the ball between the lines and runs at a central defender, it's always a chance to do damage. In those situations (granted, only from what I've seen and I haven't watched all his games), he tends to make the right decision without fail. He marshalls the striker onto his weak foot when isolated. He sends the striker towards the middle when he sees a potential overlap and avoids a disadvantage by forcing the striker into help defense.
These are little details that don't get as much attention as a crunching tackle, but he does them almost all the time. Always makes the right decisions. Players like him would flourish under people like Guardiola (or Klopp in his case).