So basically idea is, make stone drop little higher or more ways to obtain them.
For upgrade system make the bonus defences/dmg from upgrade higher in lower level and decrease that as you upgrade it more.
Example
Think this is how it is now from +1-5
+1+5+6+8+10
How it would be is like
+10+8+6+5+1
This would fix pve problem and total defences would be same.
If this idea goes through, veterans like Sendoku could help out how to make it balanced