There's nothing "special" about the scientific method It simply describes a model for the way the universe works. If you believe that model (which as a scientist I do, even though I recognize that there are a few 'philosophical' leaps required), it becomes a powerful way to understand how things work.
As a rationalist therefore, if I can adequately explain why a kettle of water will boil when I place it on my stove, then I should be able to use the same methods to understand evolution, the age of the earth, the formation of the universe etc etc.... I know many religious people agree, however, it still seems that at some point, they effectively say "well god did that" ...whether it be at the evolution stage (for creationists) or at the big bang stage (for more the more "enlightened"). That just seems inconsistent to me. Why would you use the evidential and deductive approach of the scientific method for almost everything but then stop using it at some arbitrary point because of your belief system.
The best answer I've heard (which I still think is rubbish!) is Steven jay Gould's non overlapping magisteria (NOMA) concept, that metaphysical ideas simply can't be addressed using scientific methods. It seems that the boundary between metaphysics and science can be arbitrarily drawn, depending on your initial beliefs...hence my skepticism, that this is a viable solution.
As to your comment about "history repeating itself", as I said at the start, there is certainly nothing special about scientific method, except that it answers questions in the logical and predictive way required for science. I'd argue that as older 'belief systems', religion and magic offer less in the way of
predictability. I can't see modern technology or pharmacology being arrived at through either of these systems. Of course, believers in these systems will argue that there are things that science cannot offer.... I guess that's ultimately about what you want from the world. I'm very happy using science as my framework for life... others seem to need to feel that the universe contains some intangible mystery.
great question though!