PCR is a great tool, and it's absolutely been a transformative research tool. But it's just one tool out of a catalogue of many others. It can't answer all questions. Genes and gene expression are just one part of a much bigger picture, and there are many other techniques which are just as relevant for exploring biological systems.

You rarely see PCR used in a research project in isolation. It's just one tool amongst many others, and for the most part you can't just look at gene expression and assume it has any functional effect. You've also got to demonstrate the downstream effect through other techniques, such as Western blotting, ELISA, LCMS and others, and even then you have to show that the expression products themselves also have an observable functional effect.