I know I'm a bit late joining this discussion but for what it is worth:-
Have you noticed how many web sites are moving away from a left menu, they are now appearing on the right, I believe this to be for the benefit of screen readers - would a sited person read the main navigation every time they went to a page or conciously think to skip it? No, so why should someone using a screen reader. Does this cause an issue for languages that predominantly read from right to left unlike English that goes from left to right.
The other point I would like to make is that we are in Education -we still have a lot of 15inch monitors (small), if you take up your available real estate with a navigation menu on every page it makes hard work for your students with scroll bars.
I personnally like the bread crumbs and think it is a positive step that should be embraced. As for pop up menus - no, do you know how hard those things are to click on if your hand shakes a bit or your mouse ball needs cleaning.