Not a thesis template at all, but great ideas and it sheds some light on how to get decent typography.
On a side note, I think it would be great to have a good WYSIWYG TeX editor for office/basic user level of proficiency. Typesetting does matter, it profoundly impacts reading, which is particularly relevant when you're giving 300+ pages of your hard work for someone else to read. It would be very good for everyone to get decent default typesetting. Unfortunately, our alternatives are:
* Word/typical word processors, which are are horrible at typesetting;
* TeX, which is good, but it's hard for most people and has an aura of complexity (it's code, after all...);
* Publishing software, such as Adobe InDesign, which are indeed great at typesetting, but only if you know what you are doing. This is professional software, which is clearly not aimed at common users.