Just out of curiosity, why do some people or clients want to start a website from scratch? Like wasting time writing up  JavaScript codes or cracking heads on what functionality they want.
Why people cant go for open source and extend its functionality or stick with simple websites and avoid flashes? who does flashing sites anyway this days?( unless you are into ecommerce)

Unless you can employ a web master inhouse who can maintain your website and fix bugs when they occur , then there  is no point asking for a website from scratch

Your question is like asking why I should get a toyota (mass produced) over a ferrari (customized):

1) You have more control with code from scratch
2) code from scratch tends to be and look more professional
3) any business worth its salt understands the need to be unique, hence wanting a site from scratch
4) Many of the so-called templates take so much time customizing to your taste that you might as well code it from scratch.

These are a few of the reasons why I encourage my clients to go for a site tailored to their needs, provided info on the site isn't updated regularly. If it is updated regularly, I immediately offer them CMS pricing.