All of those QBs have been mediocre for years, with a tendency to choke in big games (Flacco excepted). Passing yards alone don't get you much if you can't win big games. And Kap isn't being paid like one of the greats. He's being paid like an above average QB in today's NFL.
I'm torn on the extension. It's a lot of money. But it's highly unlikely the team was going to let him walk after this year unless he absolutely fell apart this year. It's clear the team believes he's the future, so save some money longterm by signing him now.
Let's turn it around: if the Hawks could extend Wilson this year, with one year remaining on his deal, would you be in favor of them doing it?
The QBs you call mediocre have shown skills like reading defenses and going through reads. Unfortunately they have been on teams that have not been near as good as the 49ers. The 49ers really put themselves in a bad spot by not drafting a QB. I guess they are sold on Kaep, most folks find that strange.