Prototyping PCBs are the way to go only up to a certain level of complexity of the circuit. In fact, they are good only for fairly simple circuits. Wiring all the connections with individual wires quickly becomes a hell as the circuits get more complex.
On the other hand, they allow you to make and fix mistakes. There is much less tolerance for mistakes with designed PCBs. It may take more than one iteration of designing and ordering to get it right, meaning wasted time, even if it's cheap (which it is).
Homemade PCBs are in the middle, I guess. They take less time and (arguably) money to produce them and fix mistakes, but require effort to make them and some time for the trial and error to get the process right.