Neo-Scholasticism and modern philosophy ceased being puzzled by agent causality, which was a very pronounced philosophical problem until we collapsed into ignoring it. The basic problem is that our simplest account of agency – i.e. some sort of transfer of “oomph” from cause to effect – can’t work. This transferred oomph is either the agent or not: If not, then oomph obviously doesn’t explain agent causality and if it is then we hit the obviously false dead-end of claiming that the agent literally turns into its effect, i.e. we claim that hockey players and sticks literally transform themselves into pucks and then travel across goal stripes. Explanations of agency as transfer are thus either nonsense or non-explanations.
And so while Scholastics tend to say that the scientific revolution threw out final and formal causes but kept agent causes, this doesn’t go far enough. Agent causality was ignored too, replaced by instrumental or quasi-material causes like force or energy. And though we raise the logical possibility of these things being instruments it is hard to see how there is even an in-principle possibility of science articulating what force and energy could be instruments of. If science is a complete account of nature then it is occasionalist; and if there is agency in nature then there are more intelligible accounts of nature than can be provided by natural science. Scientific Naturalism dies either way, and the only models we have for dealing with either possibility are Scholasticism or Early Modern Rationalism. If you want to avoid either Thomism, Leibniz, or Malbrancian Occasionalism, good luck with that.