Descartes was arguably one of the greatest minds in human history. He revolutionized philosophy and made some of the more important advances in mathematics of anyone in his century. Why, then, was his physics, to which he had devoted much time and energy, so deeply flawed? It would seem that a man of his mental stature and level of commitment to the pursuit of physical knowledge, was bound to hit on some important discoveries. It cannot simply be that he had some odd views about metaphysics. Take Johannes Kepler, as a foil. Though Kepler ascribed to some strange metaphysical principles deriving from his sun worship, he was still able to come up with three correct laws of planetary motion in the course of generating scores of bad ones. What prevented Descartes from generating some gems of truth amid all his falsities?
Though, of course, there is no way to answer this question in any definitive way (perhaps he was just unlucky), it seems highly plausible that Descartes' method itself ultimately doomed him to failure. Descartes was obsessed with the idea of clarity and certainty, probably in large part because of his disgust with the obscurity of Scholastic philosophy and science. In pursuit of utter clarity and certainty, Descartes attempted to turn natural science into a kind of mathematics, a prioristic and absolutist. In other words, he wanted science to become (1) a matter of logical reasoning rather than observation (an a priori, rather than an a posteriori exercise), and (2) a matter of incontrovertible proof, rather than likely, and perpetually revisable, conjecture. Unfortunately, science simply is not like that, as much as we might like it to be.
In his quest for a certain and absolute science, Descartes presupposed that his physics must derive from clear and distinct ideas of the mind. In science, however, we cannot always clearly perceive how hypotheses might work, or even what they really mean, until we have played around with it for a long time. Science as a project is heavily dependent on vague intuitions and brilliant guesses, which only slowly develop into clear pictures of the world. In Descartes' case, what his dependence on clear and distinct ideas prevented him from doing, was developing a plausible dynamics of matter. His insistence that all of physics derive from the property of extension (because that was the only clear and distinct idea we had of body) precluded him from exploring the concepts of force or energy in any useful way. These were the problems, however, that needed useful treatment at this time.