Well not to try and rain on your brainstorm but most complex ICs already use multilayer construction. In production many 'masks' are used to deposit the various materials layer by layer to make the complete IC. Also a limit to IC density seems to be the heat dissapation limits. Already VCC voltages have migrated from 5 volts down to just over 1 volt in the latest Intel designs. Less voltage = less power consumed = less heat produced. Having more cores stacked vertically would only make the heat removal more difficult.