Thanks for the response, Jan. That does make sense that v2 has been discontinued, I just wish, then, v3 worked well with Joomla 1.5.x.
I did find a work-around for it: I had to write some PHP so the upgraded MooTools loaded in the frontend of my site, but not the backend. This allows me to use JoomDoc and also keep my fancy javascript menu, so I'm happy that I was at least able to script an answer for myself.