Well, now I have to link this DC: http://dresdencodak.com/2009/08/06/youre-a-good-man-charlie-darwin-2/

(Interestingly, the author, Robert May, after presenting these quotes, goes onto suggest that "Wilberforce, had he possessed an all-encompassing knowledge of the science of his day, could have won the debate. The Darwin–Wallace theory of evolution, at that time, had three huge problems.")

Not a surprise at all. Most major new paradigms have huge gaping flaws; this is one of the core theses of Paul Feyerabend's brand of philosophy of science in works like Against Method (eg. look at his analyses of major flaws in Galileo).