Ok Ok, I give up
I think if you're thinking clearly about the problem, not defending one side or the other, the answer is obvious. The gaps in the record contain almost all the biological change that the theory of 'little steps' is supposed to explain, occurring at the origin of most species. Evolution actually proceeds by big steps (the dirty truth). The chain of connection from species to species is still obvious, it's just that the steps between them are big, separated by long periods without change. It's deceptively called "punctuated equilibrium" (not 'big steps' which would actually expose the problem), invented by Steve Gould and Paul Eldridge in 1972. Not too bad a summary is available at http://www.talkorigins.org/faqs/punc-eq.html.
Most scientists have been trying to hide the real truth ever since, saying stupid things like "that's what Darwin meant all along", and the "fitness landscape must just have that profile" etc. Blaming it on the Deity, on the other hand, having him intervening again and again and again, at the origin of every species in the long long chains of them, makes him look stupid or at the very least indecisive. Worse still, God is then portrayed as a major interventionist strangely uncaring about *us* and our squabbles. If you understand where the gaps occur (many coordinated changes happening rapidly in a single niche, local growth spurts), how they occur is obvious.