Why do mitochondria waste energy?
Its because NADH is a powerful reducing agent. If you leave high concentrations of NADH in the cell, it would actually wreak havoc on the cell.

This is actually the reason why peroxisomes just remove FADH2s because they find no use for the extra energy and simply remove it. 

So heres the simple answer. Energy is not always a good thing, because stability also matters. ATP is simply a good way to store and convert such energy.