"Re PE v. gradualism, your problem is you apparently understand neither concept. Gradualism is descent with modification over millions of years, PE is same in small groups in much shorter leaps, thus supposedly "explaining" the embarrassing lack of transitional fossils. Yet in either case, transitional fossils would have to show up somewhere, and they simply don't exist."
I think that you should read this article.
It explains that the origins of PE were based on the speciation that has been observed in modern species (neontology). Neontological species appear to be more the result of splitting of daughter species from a larger population. This would be a good explanation why transitionals would not be all that common. You are right that they would occur in small isolated populations in shorter periods of time. However, this is not different from but a refinement of "descent with modification over millions of years."