Though in theory HTML+CSS can be used to typeset page based material (e.g. http://www.w3.org/Talks/2013/0604-CSS-Tokyo/), I would stick with some other format that can be easily be converted to HTML (I personally use LaTeX for lengthy documents, Markdown for short ones). If you are good at programming, and willing to invest in developing tools to convert your own HTML format to other formats later (it is likely going to be necessary), then go for it. You can be the leader!
The main disadvantage of HTML is the lack of semantic tags. Perhaps an XML with some good XSLT that spits out HTML is better for organization.