HTML5 Boilerplate is great if you just work on a few projects, because it is easier to delete things than remember them.

If you work on new projects fairly frequently, it's better to develop your own boilerplate as a starting point. This is what I do and it saves a bunch of time.

So I understand this author's complaints. If you make web sites (not web apps) there is quite a bit in HTML5 Boilerplate that just isn't for you.

All that said, my biggest complaint is that it is good. So good that it has probably meant that other, more project-type specific HTML5 boilerplates don't seem to exist.

edit: A cool tool for HTML5 boilerplate might be a "build custom download" similar to what jQuery UI has.