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I'm not certain you could have successfully explained the relativity theories, let alone quantum mechanics, to scientists in Newton's time.
If you gave them the equivalent of a modern university education in physics, you most probably could. But it's true that you cannot explain quantum mechanics to someone who is not familiar with Newtonian mechanics, matrices and PDEs. That's a couple of centuries of gap you'd have to bridge.
But even if we could say that brilliant people have such great minds, no matter the century they existed in, it's not only a problem of (counter-)intuitiveness.
I used the term logic, not intuitive (or worse: obvious) because logic has a universal quality to it, independent of the sophistication level of the person.
Saying that light can be seen as a wave or as a particle though, is not so so unlike the early christianism's theological disputes around the holy trinity's composition.
The experimental results are what they are, and the equations are pretty convincing. And the equations and experimental results agree that there is no fundamental distinction between waves and particles. I fail to see how that's any weirder than the fact that ice cubes and water are made of the same kind of molecule, despite having radically different physical properties.
There is also another point: the scientifical methodology still in use today is absolutely useless in face of a new phenomenon. Say, a parallel universe. Partly because of the technical means available, partly because being inside a system makes it very hard to get a birdeye view of its functioning, we're doomed to advance blindfolded.
We notice some weird behaviour in some CERN experiment, and start building theories as to the cause of it. Theories are built on the base of what we know today, hence faced with something totally new, very different, or overarching, there will be little chance of figuring it out (I'll attempt a class-difference example: imagine someone barely familiar with powder guns and suddenly having to deal with a nuclear bomb; or better, an F22 attack on a tribal army in medieval Africa).
If it interacts with our experimental apparatus in a reasonably consistent fashion, we can build a model for how it behaves. It does not need to be the correct model, or even to have any justification from first principles. "Black magic empiricism" will allow us to get a rudimentary handle on its behaviour. And once we have a rudimentary handle on its behaviour, we can begin to construct testable models. From that point out, it's a fairly routine exercise to reconcile them with existing models - that's what physics has been about for the last couple of centuries. Assuming, of course, that there is a Theory of Everything. But as working assumptions go, that assumption has done us a lot of favours.
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