In our recent spoof posts about Australopithecus erotimanis, we tried to make the point of how challenging it is to infer why traits found today evolved or, even more problematic, to infer this from fossils. This raises several fundamental issues, and they are ones that Charles Darwin addressed even before Origin of Species: explaining the nature of function from observed traits, explaining the fitness effects (for natural selection) of traits past and present, and explaining relationships among species (taxonomy).
Darwin didn't have all the answers (and neither do we), but he did introduce a method into biology that he applied to all of these questions (and so do we). A very fine book, now about 50 years old, by Michael Ghiselin, called The Triumph of the Darwinian Method, goes in great detail using Darwin's own work, to show how transformative and powerful this was, and how Darwin used it in all the many contexts of his writing and thinking. Of course, legions of books and articles have adopted and reflected this approach to the present day.
Darwin didn't proclaim a method and then use it, but adopted and adapted the 'hypothetico-deductive' scientific method that had been developed over the previous century or so, for sciences based on concepts of 'laws of nature', as a way of identifying those laws and testing data in connection with them. It was a framework for evaluating the empirical world.
To do this, to a considerable extent Darwin tried to show that life followed 'laws'. So he didn't invent the method, but he did show more definitively than his predecessors, how it could be applied to life as well as planets, ideal gases, and so on. The key was the assumption that life was a law-like--he compared natural selection to gravity, for example--descent from a common origin.
Given those assumptions, he interpreted both species formation and variation, adaptive functions of traits in fossils and in comparative morphology, taxonomy, biogeography, ecology, and so on. From barnacles to earthworms, orchids and facial expression, he applied the selective, divergence framework.
There were mistakes, and one could go on about them, because some were serious. To us, the most serious is that he took too strongly the assumed 'laws', so that his explanations are sometimes too rigid and in some instances too teleological or even near-Lamarckian--directional evolution, for example, by which a fossil or barnacle was explained as being on the way to some state.
When we (that is, anthropologists who know something) try to explain fossils, like the Australopithecines we have just had some fun being satirical with, we have to try to understand all the central issues--taxonomy, function, adaptation. Given the many problems involved in reconstructions, the conplexity of genetic control, the elusiveness and non law-like aspects of natural selection (versus genetic drift, for example), the incompleteness of data, and much more, it is no surprise that conclusions have to be tentative and assertions circumspect.
One of the main axes that we grind on MT is that we feel that there are many pressures of diverse kinds that encourage us not to be sufficiently circumspect, and to claim far too much. This gets attention, and grants and promotion, but it can mislead science, when people take distorted claims as true and try to build on them.
Still, while it's fun to have fun with fossil claims, and fun to lampoon the hypersphere of our media-driven science circus, the problems are real and respectably challenging. Perhaps much more than the public--or even many professionals--actually realize.
Darwin, by the way, was often far more circumspect than is the usual case today. He wanted to be right, of course, and didn't always exercise or express enough caution. But he did frequently acknowledged where he was speculating, and so on.