Prototype designs often look ugly, because they are optimized for performance, not looks. Your initial effort should always be to try squeeze the ultimate performance out of the circuit and then see how close you can get with an actual pcb/production layout. Your prototype evaluation serves as a goal to work towards with your pcb design. Often, there will be a reduction in performance going from the "dead-bug" type layout to conventional pcb layout.
It is up to the designer to decide how much degradation will be acceptable. That is a good reason to start with the raw-copper-clad pcb prototype to see what is possible when you minimize factors that may limit performance.