(Edited at 11:50am after Coleman pointed out that the BU site does indeed have more coherence than I'd seen at first ...)
One thing we have to always keep in mind is that we're dealing with a different design problem than a lot of universities.
For example, in the eduStyle blog comments referenced above, a poster mentions the Boston University site as "B-U-tiful." And the home page is pretty nice; just swell, in fact. And there are a number of underlying pages that are reflective of that design. But a pretty huge number of subsites on the BU site have no relation relation to the home page design or the 'official' standard page design (which is clean and nice itself).
A homepage redesign is a one-off. The challenge at UNL is that we're trying to develop a well-engineered design that works for our audiences at all levels, giving them quick, understandable access to the information that they're seeking. That's why we start with the most ubiquitous page design, and not the home page.
Robert J Crisler
Manager, Internet and Interactive Media
321 Canfield Administration Building
University of Nebraska-Lincoln