I'll comment on the inclusion of Prototype within selenium: Prototype made its way into the selenium code because some developer(s?) liked the Ruby style that it lends itself to in our JavaScript. But this was never a decision based on a particular version of Prototype with a particular user-visible functional goal in mind. Once we added proxy injection mode, we were then injecting selenium JavaScript into user pages, and some of Prototype's more invasive aspects (e.g., the redefining of Object!) became troublesome in terms of their unexpected interactions with user pages own JavaScript. At that point, there was an effort to remove the more bothersome aspects of Prototype's code from the selenium code base. What was left was considered sufficiently benign as to not be an issue.
So what we have today is not intended to be "based" on any particular Prototype version. Because proxy injection mode is an important part of our plans moving forward, I think it's unlikely that we will in the future use any JavaScript framework which might introduce incompatibilities with user code.
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