Front-end displayed badly after upgrading from 3.5.x to 3.6.0

Upgrading from 3.5.x to 3.6.0 is not an option at this point to existing sites. The upgrade process in Newscoop after the themes implementation has been tested only against sample templates and sourcefabric.org, but sourcefabric.org has basically the same file structure as the sample templates. I tried upgrading a different site (provided by one of our users) with a different structure. The upgrade process finishes successfully but the front-end does not work. I was trying to find out what the problem is but it seems to be not only one but different issues that need to be fixed.

Evaluating the possibility to upgrade from 3.5.x to 4.0 must be done, if this is not doable then documentation must be provided indicating 3.5.x users how to switch to 4.0.