Although my opinion is unsubstantiated, the biggest problem is the barrier of knowledge : it takes longer and longer to familiarize yourself with an increasingly growing body of literature. Second, the low-hanging fruit tends to be picked, leaving researchers fighting for the few undiscovered scraps the remain. Third, papers are getting longer and more technical, with more data and co-authors. Forth, much longer approval times, high submission fees, and much higher rejection rates. Research seems to be a team effort now, of many people collaborating over years to publish papers that are very lengthy and technical that reflect only incremental progress in a field.
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I think there is always low hanging fruit, you just have to know where to find it. Agreed that publishing papers, especially in top conferences, takes more of a team effort now.
I hope we don't train our young scientists to go after low hanging fruit _exclusively_.