This past weekend, I read in the New York Times that there are no weaknesses left in modern evolutionary theory. Now this from The Scientist. (emphasis all mine).
This theory of evolution is really a framework for thinking about change in the living world. It provides no specific guesses for the kinds of traits that may exist, no strong requirements or prohibitions on how they may interact to make a complex organism or ecosystem, and no commitments to how innovation can occur. Even the problem of how a differentiated population ultimately divides into two distinct species (posed in the title of Darwin's seminal work) remains a major technical problem in evolutionary biology.