if it could would somebody have written it already?
I have the same problem here, running 10 sites before 3.6 and we have to stick to php4.3.10 untill I know how to migrate 10 sites in a very short time. So best solution: do not upgrade, second best, buy a new server and migrate to there site by site.
Different sites different approaches. What will happen if some of them uses patches, changes in the kernel, changes in the standard templates? Then you need to re-view all things and make upgrade step-by-step so all kind of automatic scripts will fail. With current state of eZ publish is difficult to automatize it. Any way if your site setup is clean and properly and you have backup then update should take less then 5 min (take the steps).