Shock - websites should be built for humans, not computers!
In this article Links are dead - long live links! Brian Turner points out what should have been obvious from the start. Websites should be built for people. Duh!
Whatever site you're building surely you want to get a human to interact with it. You want your users/visitors/customers to do something for you weather it's use your software, or part with cash. So, why on earth wouldn't you build your site so that they can get their way to what ever you feel is the end point of your site.
The old way of building sites is the reason why so many brand websites have been caught out cheating the search engines e.g. BMW Germany. There site was built for customers, but the search engines couldn't see it. So what are they to do but cheat. The all powerful search engines can't have it all their own way.