WCM tip #28: Design Manager: easy start but limiting if you know what you're doing. Build .master yourself
Design Manager is one of the new capabilities that SharePoint 2013 offers for building public-facing websites. Using Design Manager SharePoint 2013 allows you to use your static HTML design files as a starting point and piece by piece implement your website’s functionality in them turning them into Master Page and Page Layouts.
Although Design Manager allows you to quickly implement your user experience in SharePoint, if you have experience with SharePoint, you will quickly find out that Design Manager stands in a way of you implementing the branding the way you want it. Design Manager simplifies the process of building Master Pages and Page Layouts by enforcing a certain way of working a part of which is using HTML files as intermediate format for generating Master Pages and Page Layouts. The markup that you enter in the HTML files is not the markup that you will see in the generated Master Page and Page Layout. As a result it will be difficult for you to find the reason for should the things go wrong. Additionally Design Manager injects markup into the generated Master Pages and Page Layouts and there is no way for you to control it.
If you are new to implementing branding in SharePoint 2013, you might want to use Design Manager in the beginning, but eventually you will be better off by learning the ins and outs of building Master Pages and Page Layouts as it will allow to build better public-facing websites that are optimized for performance, accessibility and Internet search engines.