Make this one option. The other option should be one HTML file per chapter (or subchapter, or thereabouts) for the people who want to use the browser's bookmark functionality to pick up where they left off.
> no headers and footers on every page
Footnotes, OTOH, are fine if you make them links in both directions (to the note and back to the body text). Both HTML and PDF can do this, and it makes it so much less of a pain in the ass to actually read the things when you know you won't get lost.
Make this one option. The other option should be one HTML file per chapter (or subchapter, or thereabouts) for the people who want to use the browser's bookmark functionality to pick up where they left off.
> no headers and footers on every page
Footnotes, OTOH, are fine if you make them links in both directions (to the note and back to the body text). Both HTML and PDF can do this, and it makes it so much less of a pain in the ass to actually read the things when you know you won't get lost.