Thanks LordPants.
It could be easily built into the UI (user interface), that ALL cards can stack. Simply, when you mouse-over a stack, it will tell you
1) how many are in the stack
2) how many can still be activated...
As for upgraded and non-upgraded stacking, I see the problem with this. But my solution is this:
In a stack, the upgraded cards always are on the top, and therefore, when the stack is targetted by a Deflagrate/Explosion or Steal etc. The upgraded card would be targetted.
Same with Pillars and Towers. Since a tower functions EXACTLY like a pillar does (except the +1

or +3 random quanta on the turn you play it).
This would make
1) Earthquakes a lot more dangerous.
2) Protect Artifacts a lot more useful.