And certainly stamina should have an effect on FT shooting. It does in real life.
It really isn't. I'd say that it's acceptable but by no means is it a perfect system.
The skills work fine. It's the manager's job to develop the player the way they want -- don't expect to be given a freebie because "that's what happens on average". Not to mention that if a pick a bunch of random high school or amateur players, they won't be shooting .700 on average, I can guarantee you that.