It can sometimes be comforting to know that the universe imposes fundamental limits on how how efficiently computation can be done. Comforting because IIRC we've still got at least 15 orders of magnitude improvement available. But while I'm sure you're right that we're going to be able to switch to different materials (or maybe away from transistors entirely) when progress in silicon runs out we might have to expect an interregnum while other computational substrates are developed to the point where they can provide higher performance.

Stacking is certainly a thing and it's good for memory (see AMD's newest graphics card) but power dissipation provides limits in terms of how much high speed logic you can put under a given area.

http://www.anandtech.com/show/9266/amd-hbm-deep-dive