Pee pads are more about convenience. Most people have jobs and/or school and are unable to take their dogs out every few hours. My two won't even step foot outside if it's raining or cold. I don't like taking them out in the summer as the concrete gets extremely hot.
I don't really use a crate (although we have one and Brooklyn occasionally gets in it) so I can't really speak on that issue.
I must admit, I think it's funny how you criticize those who use pee pads and crates and advocate to "let dogs be dogs" but in the thread below this you mention having to hire a behaviorist for your dog.