There is a fairly clumsy attempt to answer Thomistic criticism of 'intelligent design theory' at "Uncommon Descent". As someone of broadly Thomistic leanings I can't help but make some points, despite knowing that they will do no real good.
(1) I have no clue what is meant by saying, "in Thomas Aquinas it is well clear that the formation of human being is a rigorous top-down process of manifestation that starts from a designing principle (spirit), pass through an intermediate modality (soul) and finally arrives to organize a corporeal entity (body)." This is not how St. Thomas conceives the formation of a human being, if by 'formation' we mean 'forming'. If we mean 'informing', St. Thomas's conception is not ternary as the author suggests but hylemorphic, i.e., binary components (form and matter) in a unary composite. St. Thomas is indeed creationist about the human soul; he thinks that human intellect cannot be generated by incidental causes. This is not ID, however; the human intellect is not 'designed' except in the sense that it is an intelligible effect, and God's existence is established on entirely different grounds.
(2) Yes, St. Thomas thinks that God is intelligent; this is neither here nor there on this question, because ID is not merely the claim that there are intelligent causes, or even one intelligent cause, but that we can have direct inference from particular natural objects to an intelligent artisan that has imposed characteristics on those objects that make them what they are and are indicative of intelligence. (It simply doesn't matter whether the artisan is treated as 'internal' or 'external' to the object; in Thomistic terms this is still an extrinsic imposition.) From a Thomistic point of view, this is to say natural objects have their natures as accidental forms and is incoherent. The Thomistic argument is not that ID goes wrong in thinking that there is an intelligent cause, but that its conception of natural objects is inconsistent with very basic Aristotelian principles, scientifically misleading, and theologically inadequate from the point of view both the doctrine of creation and the doctrine of providence.
(3) The author makes a common ID error, namely, he goes back and forth between 'laws' and 'necessity' as if they were the same thing.
(4) The worst thing the author of the post suggests, from a Thomistic perspective, is when he says, "What is this CSI but the tool to get the final cause and allow the particular purpose or end of exchanging oxygen? The terminology is different but the concept is quite the same." The concept is not at all the same. The final cause in Thomistic terms is the principle that makes a cause have this effect rather than some other effect. There is no need to have a "tool to get the final cause," nor can 'final cause' be conflated with purpose or functionality; from a Thomistic point of view and in the Thomistic sense of the term, without final causes there would be no dispositions, powers, capacities, tendencies, inclinations, capabilities, abilities, physical laws, or efficient causes. It doesn't need to be shoehorned in, and especially not by something as controvertible as CSI; if we concede the existence of CSI for the moment, CSI would presuppose final causes, not vice versa, and the final causes in question wouldn't need to be considered in terms of 'design by a designer'. You don't need to presuppose CSI, or any sort of design theory, to have final causes in the Thomistic sense; if the point of ID or CSI is to give you final causes in this sense, they are both completely otiose. It is this very suggestion that shows just how alien ID and Thomism are to each other. Yes, in some sense of the term Thomism is teleological, and in some sense of the term, so is ID; but the senses are not only different, they are mutually exclusive.
(5) ID is a mechanistic theory; it is precisely this that from a Thomistic point of view puts it on the same level as reductionistic materialism.
(6) No Thomist is going to be particularly impressed by the argument that ID is superior to Thomism because it has greater "anti-Darwinian power," as if that were some end-all and be-all of philosophical reasoning. Thomism as such has no particular interest in being "anti-Darwinian"; indeed, if the choice is between 'Darwinism' and ID, most Thomists today will generally take 'Darwinism' as the less pernicious and misleading approach to the natural world, and those who don't will still not regard "anti-Darwinian power" as some sort of touchstone of adequacy. It is also pretty thoroughly impossible to imagine Thomas Aquinas, if he were living today, using ID "to better refute Darwin" -- there is no good reason to think that Aquinas would want to refute Darwin in the first place. It is far more likely that he would regard ID theorists as merely confused. And that, indeed, is how most (although admittedly not all) Thomists regard them.
(7) The author's argument is not even coherent; he claims that Thomism and ID are compatible because they have the same basic view on this point and then says that the two are compatible because they are wholly different things. The post does display very nicely just how slippery ID use of the term 'design' is. For instance, we begin early on with "Ideas are designs in the divine intellect." Well, one can consider ideas to be designs or plans of a sort; but they are remote exemplar causes established on the basis of epistemological considerations about intelligent productive causation, not something to which one can directly conclude or something from which one can draw inferences about what is possible or impossible for natural things to do. Then there is design in the sense of complex specificity in the object itself. This is obviously not the same sense of 'design'. Then this concept of design is conflated with 'teleology', 'final causes', 'functionality', and 'purposes or ends', as if these were all the same thing. Then design in this sense is said to be purely a matter of logic and mathematics, despite the fact that there are no final causes in logic and mathematics as such. We see similar slipperiness in characterization of the opposing position. At one time it is Darwinism; at another time evolutionism; at another time materialism; at another time anti-creationism; at another time rejection of teleology; as if all these things were the same. Thomism, like any scholastic viewpoint, is big on drawing careful distinctions. ID theorists who actually want to argue that there is any common ground between Thomists and ID theorists should take the trouble to start there. (An amusingly common refrain in the comments thread is that, whatever value Thomism has, ID is easier for most people to handle. Of course it is; positions that conflate everything with everything else will always be easier for most people to handle: fewer things to keep track of, and less hard thinking to do so.)