HTML and CSS for typesetting?

No, just no. HTML and CSS were designed for looking good on screen, not paper. Although there are CSS styles for page printing, using a medium for a purpose other than its original design will at best be an overkill (if it works) and in most cases a utter source of frustration.

The obvious choice seems to be LaTeX... I wouldn't be using all its advanced features.

This is the basic misconception. You will use all advanced features even in a humanities thesis. You will have inline references, bibliography entries (bibtex), links to bibliographic entries, figures, title pages, perhaps even tables etc. As you see, you are going to use much of the advanced features of LaTeX, regardless of your discipline. LaTeX has a increased initial learning curve, but in the long run it is worth this time investment.

Conclusion: Stick to LaTeX.

HTML and CSS for typesetting?

No, just no. HTML and CSS were designed for looking good on screen, not paper. Although there are CSS styles for page printing, using a medium for a purpose other than its original design will at best be an overkill (if it works) and in most cases a utter source of frustration.

The obvious choice seems to be LaTeX... I wouldn't be using all its advanced features.

This is the basic misconception. You will use all advanced features even in a humanities thesis. You will have inline references, bibliography entries (bibtex), links to bibliographic entries, figures, title pages, perhaps even tables etc. As you see, you are going to use much of the advanced features of LaTeX, regardless of your discipline. LaTeX has an increased initial learning curve, but in the long run it is worth this time investment.

Conclusion: Stick to LaTeX.