Simon Willison’s Weblog

MooTools is not compatible with any other javascript framework. If you "definitely need to work with prototype" (which you don't, since the frameworks each provide all the functionality you need to use only one or the other) then learn how to do what you want to do in prototype. Otherwise, learn to use MooTools to do all the things you want to do. They simply do not work together, and I promise they never will.

— Tom Occhino