Hmm, I agree, the answer to the question posed varies a lot between different fields. That's another aspect of these articles that I don't like: they talk about "problems with science" as a whole as if it were a monolith.
Yeah, I totally agree. Within fundamental physics, I think you're totally right that people were, in a sense, "spoiled" by the great revolutions of quantum mechanics and relativity, and seem to think the next revolution is right around the corner if they can just gedankenexperiment hard enough in their heads. But it probably isn't. It's probably going to be a long slog of hard work and incremental advances that will be necessary to set us up for the next breakthrough.