Finally, it seems that hope is on its way and we may finally be rid of the Mootools 1.1 "curse". Have a look at this discussion:
In light of these recent developments, in seemed that the obvious way forward was to aim for a solution in Joomla 1.5.16 (or later if nec.) based on Mootools 1.2 with the newly developed compatibility layer. This gets us a lot in terms of allowing developers to work with MT1.2 while greatly reducing the chances of breaking existing sites using MT1.1 scripts.
I am currently in conversation with Darren, and from what I hear, the layer is almost done. I hope to get a test copy as soon as possible! When this happens, we can (hopefully) kiss all the Mootools problems goodbye.