The main downsides to PDF are that it is not supported in all browsers, especially mobile or embedded ones and even in the browsers where it is supported, it is implemented as a plugin and so is slow to load.

PDFs open in 3sec on this computer. That seems small, but html+css pages open almost instantly.

There are lots of nice things about PDF, but when almost everything else I'm viewing is html+css it's unpleasant.