When comparing Skeleton vs HTML5 Boilerplate, the Slant community recommends Skeleton for most people. In the question“What are the best Bootstrap alternatives?” Skeleton is ranked 6th while HTML5 Boilerplate is ranked 7th.
Ranked in these QuestionsQuestion Ranking
Pro Responsive grid
Pro Style agnostic
Pro Vanilla CSS
No bells and whistles for Skeleton, it's just CSS.
Pro Media queries
Pro Includes a comprehensive set of server configuration files
These configuration files may help increase performance of the webapp.
Pro Includes Modernizr
Modernizr checks browser support for HTML5, CSS3, as well as a few other miscellaneous elements and allows for easily writing fallbacks if they're not supported.
Pro Documented and undocumented versions
To help out newcommers to either programming in general or HTML5 Boilerplate specifically, the boilerplate includes in-depth docs that help understand how things work and why certain choices are made. The documentation is highly comprehensive going even as far as to describe every single line of normalize.css that the H5BP includes.
Pro Cross-browser normalization
H5BP includes normalize.css that will help fix inconsistencies in the way browsers render elements.
Pro Performance optimizations
HTML5 Boilerplate theme doesn't only provide a base template for building your next modern site. It also has performance optimization features built into it which include stuff like html + js minification , image size reduction as well as css minification. This link here describes how to optimize your shiny new html5 site using these built in features.
Pro Optional support for XHR and Flash
With optional support for XHR, we can use techniques such as XHR eval and XHR injections to optimize the loading of external scripts and significantly reduce page load times. Alongside XHR, built-in support for Flash means that you can use your old swf/flash content on your website, where you feel you're not ready for HTML5 yet.
Con Not maintained anymore
No active development for two years.
Con Not a complete solution
HTML5 Boilerplate is basically just that, a template or a basis on which to build an HTML page. It doesn't have much mark up or components out of the box. In other words, it doesn't provide all the components and tools needed to build a UI, it contains best practices and a generall template on which to build your UI.