I suppose science is the art of the 'most likely' explanation, ether worked because, at that stage, we were using the 5 senses we had, and only mildly enhanced, nowadays we artificially extend those senses, and can see in ways that we were completely incapable of when we believed in Ether.
However, I do agree with some of your point, since I think that, particuarly in the case of Quantum-level science, everything we 'identify' is an effect rather than a cause. When dealing with Mind, you are dealing with something that relies very heavily on labels, stories and re-iterated beliefs. For example, I believe that trees were around millions of years before there were any humans to hear them fall (since the ability to recieve auditory input is an old one), and therefore logic suggests that we do not need to exist to hear them when they fall, but that is still a concept carved out of a mixing pot of personal beliefs, learning and research, and since most of those are influenced by other people, who have
their own 'mixing pot', you can soon see that things get fractal

As you say, there is no real way of proving it.