Design is not just what it looks like and feels like. Design is how it works.
Much as foundational concrete and piles define the stability and longevity of buildings, so the structural underpinnings of web sites affect their success in ways that, though not visible on the surface, are ultimately far more important than color and typography. Site structure determines how well sites work in the broader context of the web.
The methods you use to mark up pages determine whether they can be read well by software and indexed well by search engines. The logic and stability of the underlying files and directories that your web site rests on affect its functionality, as well as its potential for growth and expansion.
Attention to these behind-the-scenes structural components from the start produces a web site that will hold up over time, work effectively within the larger web environment, and adapt and grow as needed.