Vanilla is using its own framework and widgets for most of core and Scriptaculous in two setting pages (and in some few extensions).
Many extensions authors use jQuery when needing a js framework. I don't know if it is easier to use than Prototype but jQuery has certainly a better document (and is easier to compress).
Who would like to convert Vanilla to one library?
Which library to use? jQuery seems to be a good choice but jQuery UI is quite buggy; the sortable widget is not as powerful as the Scriptaculous one (but it work in IE7). MySchizoBudy thinks ext (http://www.extjs.com) could be a better choice.
And can we do more than just a conversion?
Clean-up the global scope?
Remove inline javascript?
Create an api to interact with the some part of the forum. Because some extension require the default vanilla dom structure (e.g.: quote extension), if a theme or an extension change this structure, these extension are broken. Extension that mess up the dom structure would just need to redefine some of the api function or parameter.