I'll take a hit on this. If you did not find any resources after a thorough search on Google, I would say that you are stuck in simply opening everyone's API and just consult them back and forth and look at examples.
I am really moving from Prototype to jQuery in the project right now. (Also: I'm much happier with jQuery, which has been using both for a while.) My main workflow just references the API as needed.
I would be surprised if there was such a comparison among themselves. In both frameworks, there are many ways to accomplish any given task, and in addition, they work in different and important ways. Of course, there is some 1: 1 relationship, such as “addClass” and “addClassName,” but the JQuery DOM manipulation usually works with sets of elements (which can only be a set of 1), while Prototype works with individual elements (which can be wrapped each operator works with sets).
Fortunately, both have a pretty good and easy to use / reference API.
Good luck.
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