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Steven,
Perhaps the Hydrogen atom is a bad example to highlight your point.
If we assume (or accept the "crazy" idea) that electron is a wave (de Boglie) , then it is very easy to see why we have different energy levels here.. because when the wave goes around the nucleus, the only possible orbits are those where the circumference of the orbit is the integer multiple of the electron wavelength. So the distances (and therefore energy levels, calculated from them, taking into account the electric charge and the attracting force between proton and electron) are strictly determined. And the measurements (spectrum) show excellent agreement with calculation results.
The problem are other, heavier atoms, where things are not so simple and the energy levels calculated using this simple "mechanistic" model are far from what is measured in experiment. This is because many other things affect the results, Pauli's principle is just one of those, which simply does not play any part in Hydrogen atom affairs (because there is only one electron here and we need more electrons for this principle to become a factor at all).
Otherwise, your point is very valid :-)
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