I agree there. All the fossil record can do is contribute evidence to the theory of common descent - and this it does - there is clear progression in vertebrate forms in successively dated strata, for example. One can't prove that transitionals are "direct" ascendents of their successive forms without DNA, but they can, in many cases, show a clear relation by morphological similarities.
Fossil evidence is not the only line of evidence used to support evolution, though. There is also:
1) Morphological continuity
2) Biogeographical distribution
3) Genetic analysis
4) Observed instances of evolutionary dimorphism & speciation
Inquiries along all these lines have lent support to the same scientific conclusion. This spells out, in the end, a strong scientific theory. To consider an "alternative" to evolution, one has to provide an explanation that uniquely accounts for all this information, not just a single piece. Granted, the theory isn't complete (scientific theories seldom, if ever, are), but this lack of completeness does not translate to complete uncertainty. Evolution remains the only coherent & successful scientific explanation of biological origins.
Why did Gould have to resort to "punctuated equilibrium" to explain the lack of fossil evidence for transition at the species level ?
Whether punctuated equilibrium is a real phenomenon or an apparent illusion caused by the inherent paucity of the fossil record is a genuine scientific debate, last I heard. Note that it is a debate over the specific details of evolution, not whether or not it occurred. Doubt over whether evolution occurs at a steady pace or in irregular cyclical "spurts" doesn't cast doubt on the general coherence of the theory, only some of its specific details. The specific details of every scientific theory are under constant refinement and improvement, without exception. The continual refinement of theories is not a weakness, but rather the primary strength and power of the scientific method. Such refinements can't just be stabs in the air though; they have to take into account all existing data.
You should look up some of Ichneumon's famous posts on the ERV virus DNA segments in the human genome here on FR. I'm not sure how to look up something that detailed, and I don't have the bookmark on this computer. But basically, they've found a couple of thousand retro virus DNA segments common between primate and human genomes. Since those segments are randomly inserted in the genome by infections in a single individual, that's hard core proof of common descent of these several species. The cool thing is that the farther back the species split was, the fewer common segments there are, confirming dating. Further, the older the split, the more random DNA mutations in the "dead" code there, which confirms the species split sequence and dating again.
There haven't been any good public media presented on this subject yet, but the bottom line is that we've added more confirmation of evolution in just the last few years than we've had for the last 150.
It's really pretty exciting. And the claims heard around here of "scientific doubts about evolution mounting", are just so funny. Little do they know.
Thanks for the excellent reply.