How does this compare to your ability to think of major research questions in various subfields? It's possible that it's just harder to keep up with current research, either because keeping current is always hard or because there's more stuff you have to know now compared to the past. The examples I hear the most about in physics are models for particle physics beyond the standard model, macroscopic models of gravity and dark energy, and the gigantic muddle over how high temperature superconductivity works.
I don't think I've thought really hard about questions in more than two subfields of botany. There are hard questions which seem to just snowball since Darwin's times, but from what I can tell, there's a major line of research (comparing various groups of plants using progressively complex machinery), from which theories branch off without much re-weighing after initial rejection.
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