It's true that Ptolemaic cosmology stuck thinkers in a rut for a very long time; but what got us out of that rut was observation (and simplification). Copernicus saw that heliocentrism led to a simpler model that fit observation better (ironically he wanted to recover Ptolemy's perfectly circular orbits!). In turn, Kepler's perfectionism led him to ditch the circular orbit idea to yield the first accurate description of orbits as ellipses. Yes, transgression against long-held belief was necessary to move forward, but in every case the transgression explained observation. Transgression itself is undesirable. In fact, transgression unmotivated by observation is what powers the dark soul of the "crank", who is at best a time-waster and at worst a spreader of mental illness.

Even Einstein did not produce (e.g. special relativity) out of whole cloth. He provided a consistent conceptualization of Lorentz contraction, itself the result of observing descrepencies in the motion of Jupiter's moons. The same could be said of the photoelectric effect, the ultraviolet catastrophe, and QM.

All this to say that your statement "The rapid decline in progress in modern times would seem most likely to suggest that something we are taking as a fundamental assumption is probably wrong" is unsupported. Nothing could be more popular than questioning fundamental assumptions in science today!

It could very well be that, as Sean Carroll puts it, we really know how everything larger than the diameter of a nuetron works! Moreover, we know that even if we find strangeness at tiny scales, our current theories WILL remain valid approximations, just like Newtonian mechanics are valid approximations of special and general relativity. The path to progress will not happen because a rogue genius finds something everyone missed and boldly questions assumptions long-held. Scientific revolution first requires an observation inconsistent with known models, but even the LHC hasn't given us even one of those. There is reason to think that GR, QM, and the standard model are all there is...until we do some experiments near a black hole!