Well Underscores is surely one of the best starter theme out there and the fact that has been developed and maintained by a bunch of really great WordPress developers (some of them works right at Automattic) let us imagine that the code is 100% WordPress.

At the same time I have started to not use a starter theme anymore even if at the beginning I was using them a lot (Bones is a great one too) because all of them require me to build my on starter elements like the grid system and several other feature.

Nowadays me and my there have chosen to use the Genesis framework to help us jump start the development phase and we choose the Genesis framework because, even if it is a commercial one, we are able to start with a solid codebase and with the help of child themes and common coding standard we're able to deliver the project in less time.

I understand that my answer is a bit different from your kind of request but at the same time it has been my path into becoming a better WordPress developer :D

If you'd like to start from complete scratch I've got Underscores Just go to the website, type in your Theme name on the yellow bar there, click 'Advanced Options' and add some more info if you like, then yeah, click Generate.

It will then generate a blank theme with your input, and you can start from there.

As lightweight as you can get, and stripped of all content, making it flexible.