Aravot,
I did a small test under the RocketTheme template I was having issues with, and it seems the image-rollover, and Add-cart pop-up works now with MT-Upgrade, but I still need to test it with a clone of my production site which has a Yagendoo Theme and One-page-Checkout, to see if it all works fine...
A curious thing I noticed was now the Inverse case, where having MT-upgrade OFF breaks the image-rollover... so are you planning in having VM ONLY for the new Mootools 1.2?
Thanks!