Having read over your coverage of baraminology, I'm left somewhat confused about how fossils fit into the picture. You appear to accept the existence of transitional forms (e.g., feathered theropods), but make no attempt to account for them. If they bridge the morphological gap between baramins, does this not pose a certain problem for your model?
First I want to remind everyone reading that I do not treat this blog as a real publication outlet. It's a soapbox. That's it. If you really want a careful exposition about various issues, you'll have to check my books (see right) or my published papers, many of which are online. So just because I haven't said much about something on this blog doesn't mean I haven't considered it.
As for transitional fossils, I prefer (with Wise - PDF) the more neutral term intermediate (transitional implies that there was a transition made), although I'm not very consistent in that preference. As you note, I do not deny that intermediates exist (e.g., feathered dinos here and here). In fact, there are lots and lots of really interesting intermediate forms in the fossil record: Devonian tetrapods, Odontochelys, archaeocetes, various other Cenozoic mammal series, mammal-like reptiles. There are living intermediates as well: Latimeria, platypus, velvet worms, various species of Flaveria.
What can creationists do with these things? Well, some of them are likely to evidence real genealogical relationships within baramins (although I still don't know if I'd call them "transitional" forms). The horse fossils and Flaveria would be examples; see my paper on biological trajectories for more information on that option.
Others are more interesting. I've been seriously working on a baraminological analysis of whales for the past five years, and I'm finding consistently that archaeocetes are not intermediate between terrestrial mammals and whales. I've documented some of this work in BSG abstracts (e.g., p. 10 in this PDF), but I have many more analyses that I need to sort through this coming year for a more comprehensive treatment. I think these results are very interesting, especially in light of Heaton's critique of creationism "that multiple causes are invoked to explain the same phenomena" (quoted here), that is, that we accept some intermediates as evidence of common ancestry while rejecting others. But if there really is a qualitative and quantitative difference between classes of intermediates, then that criticism would be somewhat blunted. The evidence in the case of archaeocetes is complex though, and I don't want to give the impression that their non-intermediacy is settled. I'll have to say more about that later, though, once my work is formally published.
Even if there really are two legitimate classes of intermediate forms (intrabaraminic and interbaraminic), that does not resolve the question of why the interbaraminic intermediates exist. As a young-age creationist, I'd have to confess that interbaraminic intermediates are likely to be baramins themselves and are therefore attributed to creation. I say this with one reservation: Some Seventh-day Adventists like Harold W. Clark (in his 1940 book Genes and Genesis) believe that these intermediates are "confused species" that arose by interbreeding of created species. I will, however, proceed on the assumption that this perspective is incorrect (like Frank Marsh, I find the notion of reptiles and birds crossing to produce Archaeopteryx incredible) and that interbaraminic intermediates were created by God. Why did God create these intermediates?
When dealing with God's motives, we're getting into the realm of theology, but I think the science still has something to offer. Ultimately, the question of why God created interbaraminic intermediates reduces to a more profound question: Why did God create the particular set of baramins that He did? Their similarities form a pattern, and the question is what does that pattern mean? Given Psalm 19 and Romans 1, I tend to think that creation is not just a glorification of God but also a form of communication. Given that, I think the pattern of baramins may be a complex language. At this point, that's as far as I've gotten on that work. I think if I can show that properties of language can also be found in the pattern of baramins, then I've done my job and can retire.
I definitely want to acknowledge that Darwin believed this pattern of baramins to be easily explained by common ancestry (see my chimp genome paper for a discussion of this). In Darwin's day, I would agree that the emerging pattern did look a lot like a genealogy, but I don't think that's true anymore. I think homoplasy has proved to be such an important feature that the pattern today only vaguely resembles a genealogy (see here and here). True, evolutionary theory can accommodate such new evidence (e.g., by invoking rampant gene transfer to account for the base of the Tree of Life), but I think making the argument that the pattern looks like a genealogy today only works in the vaguest sense of the resemblance. At any rate, I definitely think the complexity of the pattern opens the field for competing explanations, such as a linguistic-based creation pattern.
So how's that for an "attempt to account" for transitional fossils? Thanks for helping me put all my thoughts on this subject in order. Other questions can be addressed to toddcharleswood [at] gmail [dot] com.