As someone who did typeset his thesis not too long ago to forget all that lot of tiny tweaks I had to make to get a perfect print out from LaTeX, I would say that this project has a lot of issues. Some of them a more or less easy to fix, but some of them will be hard. Consider wrapping some specific paragraph in a \fussy / \sloppy pair, or hammering a specific float to this page, or ... (this list is really long). Not to mention bibliography tools. I don't claim that these issues are unsolvable, but the deeper you go into solving them the more you will discover that you are basically re-implementing LaTeX.

While the idea of multi-format thesis, or at least double format - PDF and HTML, is very compelling, I doubt there could be good enough solutions for that for any thesis which contains more then just text and some inconsiderate amount of figures/tables/formulae at all.