Gould and other punctuated equilibrium proponents see the lack of intermediary species as a flaw in the theory of phyletic gradualism; they see this as convincing evidence that species make bigger evolutionary leaps in shorter time frames than gradualism allows for. Gradualists actually take this lack of fossil evidence as possible proof that their theory is correct -- the incompleteness of the fossil record makes it far less likely to contain record of transitional species (KVIE, pars. 2-3). The theory of punctuated equilibrium, with its reliance on the facts present rather than an insistence on facts absent, makes more sense to my mind than the theory of phyletic gradualism. Gould's explanations extend beyond the mere mechanism of macroevolution to explain -- not with certainty, but with great plausibility -- the state of the fossil record. If, as Gould proposes, small populations of a species changed, then "the new species will only leave fossils at the same site as the old one if it becomes successful enough to move back into its ancestral range or different enough to exist alongside its relatives" (KVIE, par. 5). This is an actual explanation for the fossil record, rather than an insistence on its incompleteness as reason not to discount the theory of phyletic gradualism. Having a better explanation for the fossil record in no way proves the theory of punctuated equilibrium, any more than it disproves phyletic gradualism,...

This fact means that the true mechanisms of macroevolution will probably never be known with any certainty. Without being able to accurately trace the branching and differentiation of a species from generation to generation over a long period of time, there is no real way to know exactly how rapidly evolutionary changes occur, or when speciation takes place. It could be that whole hosts of intermediary species are missing, and phyletic gradualism could be the simple truth behind macroevolution. More likely, given the evidence available, is that macroevolution is subject to unpredictable complexities of destructive and disruptive forces, much like the fossil record itself, and leaps and pauses along in a punctuated equilibrium.
Works Cited

Gould, Stephen Jay. Punctuated Equilibrium. Cambridge: Belknap Press, 2007.

KVIE. "Punctuated Equilibrium." PBS Evolution Library. 2001. WGBH Educational Services. Accessed on 10/30/2008. http://www.pbs.org/wgbh/evolution/library/03/5/l_035_01.html

Ridley, Mark. Evolution. 3rd Ed. New York: Blackwell Publishing, 2003.