I’ve done a big system with XML+XSLT (using Cocoon 1.8.x something around two years ago). What I can tell you is that although it looks great at surface but it becomes hard to manage imho because of the inherent limitations of XSLT language. I do prefer DVSL (see http://jakarta.apache.org/velocity/dvsl/index.html). DVSL is used in Anakia, Jakarta’s documentation/site management system. In Anakia you define the content of the docs (chapters, paragraphs and so on) in XML but you use Velocity to transform it to the html docs instead of XSLT and I found it way better than XML+XSLT documenting systems such as Stylebook. Anyway, the moral of the story is: XSLT has many limitations, you end up generating XSLT friendly XMLs and it becomes hard to manage, in my opinion of course.
Sitemesh is great for managing “consistent look/feel, navigation, and layout scheme”, and the beauty of it is that you can use it with any web app system you want, even CGI! So far the best web app framework I’ve found with a relatively good balance between design/flexibility/MVC/simplicity is Tapestry.