There are plenty of ways to improve research productivity on the margin, but I don't think that's the point of the argument here. The argument isn't that research productivity is getting worse because of X, and to solve it we need to do Y. The argument is research productivity is getting worse because of X, and because X is 'the laws of physics', this slowdown is a feature of the universe, not a feature of our poor research methodologies. It's inherently unavoidable, to some extent.
The plain fact is that everything we do is limited by (1) the laws of physics and (2) the space of possible inventions. In the early days of the industrial revolution, we didn't really know the laws of physics and we hadn't mapped out the space of possible inventions. But today is qualitatively different. Broadly, research productivity is hitting diminishing returns. The key questions here are (1) how do we know this to be true? and (2) why is this happening?
(1) is touched on by a number of books and papers. You can look at progress in transportation. The gains of today are pitiful compared to the gains of 1800-1950, where we went from horses to steam locomotives to airplanes to rockets. You can look at progress in medicine. We made progress earlier by discovering that germs existed and that we should wash our hands. Equivalent gains today now take billions in drug R&D. Really the only sector where we've been doing well over the past few decades is IT, and now even that's maturing. Moore's law is dead, the gold rush for the web is over, and smartphone penetration is approaching its natural limit of 100%.
The two key readings I would recommend here are Robert Gordon's 'The Rise and Fall of American Growth' and Nicholas Bloom et al.'s 'Are ideas getting harder to find?'
On (2), I think it's worth emphasizing that electromagnetism was mostly figured out in the late 1800s. Quantum mechanics was mostly figured out in the early 1900s. The essentials of nuclear energy were figured our in the early to mid 1900s. Even though we know gaps in our physics knowledge remain, these gaps are not going to overturn what we already do know. And what we already do know really constrains the efficiency of our designs. We're not gonna make engines that beat the Carnot limit. We're not gonna make vehicles that are simultaneously (1) fast, (2) energy efficient, and (3) move through the atmosphere. We're not gonna find chemical fuels that are denser than hydrocarbons. We're never going to beat entropy in improving the energy efficiency of ore smelting. Etc.
Now, I don't mean to establish a straw man that progress is over, that innovation is impossible, etc. But I really do believe that design space is finite and there are diminishing returns in its exploration. Before you believe it, it sounds crazy and defeatist, but after you believe it sounds banal and obvious.