the arguments that overturned classical physics were arguments from gaps, very tiny gaps between the theory and the observation- of subatomic physics and orbits of planets.
The classical physics is not arguments the gaps.
It was based on observation (through either tests or evidences), with the best tools and technology that they have at the time. They didn't have the technology of the 20th century (and of course, the 21st century). Progress allowed for better tools or equipments that allow scientists to investigate what they couldn't before.
Evidences for atoms didn't first exist till early 19th century, even though ancient Greek philosophers have hypothetically suggest the smallest matters were "atoms". It was until J.J. Thomson measure the mass of the cathode rays (in 1897) that he detect a particle lighter than hydrogen that electron was first discovered. Other technology enabled physicists to detect for nucleus, and then protons and neutrons.
But it wasn't till the first particle accelerator was used that they detected particles smaller than electron, proton and neutron, the subatomic particles like quarks. And that protons and neutrons were made out of these smaller particles, ie quarks.
Take the evolution of the computers, which began with being very large computer, taking up whole floor of office building, and yet do even less than what a desktop computer or notebook computer can do today. Only with increasingly more advance technology, was computer was made with increasingly smaller electronic components, like CPU (central processing unit, or the processor) or memory, where transistors has become microscopic, when comparing to transistors of 20 or 30 or 50 years. Each year, processor makers, like Intel or AMD can fit more transistors into a single processor than 10 years or 15 years ago.
Before the iPad, was a PDA device was a tablet-like device that Apple began manufacturing the Newton devices in 1987. Newton has capability of recognising handwriting with a status, similar to the touchscreen of most mobile devices of today tablets and mobile smartphones.
It is progress that allow science to advance. And when science advanced, so does engineering or any other technology.
If you were to tell people 40 or 50 years ago, that there would be computers in just about every home, they would have thought you were insane.
Classical physics have to give way to modern physics, but not all classical physics have been discarded. We can still use Newton's law of motion or his knowledge on gravity, but we have gone beyond it with quantum physics and relativity, and number of scientists/mathematicians are trying to replace these two modern physics fields with (yet unsuccessful) string theory.
It would be remiss for any scientist today to ignore progress of science for sake of classic or tradition.
Evolution has progressed since Darwin's time, with several more new evolutionary (biological) mechanisms, but Natural Selection is still a very valid mechanism (and theory), but Darwin's original theory has since been updated during the 20th century, to take into account of mutation (another mechanism that I was talking about) and others like DNA, RNA, molecular biology, biochemistry, biophysics, etc.
And there are plenty observed evidences for Natural Selection as there are for other mechanisms of evolution, so evolution is not just a theory, because the evidences supporting evolution are what evolution "factual", as opposed to the myths or superstitions of religious scriptures.