Why are charge pumps only used for low current applications?
There are two problems with your idea. One practical, and one fundamental.

The practical problem is that per amount of stored energy capacitors are more expensive than inductors, and on top of that the realy high-capacity capacitors (electrolytic) age. 

The fundamental problem is that charging a capacitor from a voltage source is fundamentally lossy (you dissipate heat). This might seem counter-intuitive, but is nonetheless true. (There was a question about this some time ago.) Hence a flying-capacitor voltage converter, even an ideal one, is inherently inefficient. (An ideal inductor-based voltage converter is 100% efficient.)

You might think it strange that the world is unfair to capacitors, but that is our human fault: we supply power mostly from voltage sources. For current sources the inverse is true: an ideal current converter from flying capacitors can be 100% efficient, while one from inductors must necessarily be lossy.