We are using Prototype 1.5.1.1 along with Scriptaculous version 1.7.1.
Tried upgrading to Prototype 1.6 branch (along with 1.8 branch of Scriptaculous), but seems some things must have changed - more than a few things do not work when we point our files to include the new versions (firebug is throwing all kinds of exceptions).
I don't mind fixing the items, but am wondering if there is a migration page or some other documentation that explains what has been removed/changed/depreciated/etc so we can isolate and update the proper code.
There's even an elaborate update helper.