Hello,
Well, in my experience, CSS3 transformation right now is probably the slowest possible option for something like that. Right now it works best in Chrome, probably due to some sort of hardware acceleration support. For example in Opera (my default browser) it is almost unusable.
I don't know how big your screen is, on mine I could only fit 20x25 small ones and it's already pretty slow.
Here is a test:
webcodingeasy.com/my_classes/js/iso
...
Try clicking on cube panes for detransformation