Paul, first I feel that unlike some other positions, evolution is not a philosophy, but rather an interpretation of data, and takes positions that depend on physical findings and thus can be argued on the physical evidence, rather than being based on a particular philosophical or theologic interpretation, and thus being subject only to philosophic arguments, ignoring whatever physical evidence that does not conform to that view.
Next, evolution does not state that similar design must denote common ancestry, though often that is the case. Convergent evolution is well described in many cases, with the evolution of flight and the eye being two commonly described examples. As to vitamin C, it is not only confirmed by DNA sequencing that some species that cannot make their own are related, but also that some are not by virtue of the faulty gene being due a different mutation. This is the same technology used by various companies to trace where your ancestors came from.
Lastly, submarines did not evolve from whales, except perhaps in the philosophical sense.