Excellent Article. Honestly I have my own version of boilerplate & i have customized it as per my code needs.
Boilerplate comes with a minified version of Modernizr. While Modernizr is an amazing library I don’t use it in all of my projects. I rather use HTML5 shiv with conditional tags for IE 8 & below.
Also i ask my clients whether to use polyfills like CSS3 Pie for rounded corners and all. The polyfills have advantage as well as disadvantage including degrading page speeds.
Lastly to conclude, if we remove the unwanted code, the page-load time would decrease and thereby create better user experience.