actually, the CSS driven MooTools javascript engine is far more powerful than the actual vB js scripts for the menus, and you do not need any javascripts inserts in your html to make them work... so if you want to go with it, it will give you better popups and rollovers effects... you then can drop some .js from vbulletin itself when you're done.

i've done this path, and at the opposite of Princeton, it was not that complicated to execute... upgrades are to be done in a lot of other occasions anyway, so why not... there is a compare templates engine in vBulletin, that's ok. the best thing to do then is to create a child of the actual default style, and do not update it when you upgrade your forum... compare the changed templates and apply these changes to your own CSS-driven style. will cost way less than upgrade at first.

if you are the one to create your CSS driven style, you will know it by heart so when it's time to upgrade vB, you will be aware of all the needed changes anyway... the people who have problems are the ones who hire a designer and loose it before an upgrade.