naturalism’s appeal to Ockham’s razor
If you can account for everything without bringing x (here: God) into the picture, throw x out. But we do well to ask whether naturalists are really accounting for everything? Or only those things they can address with their pre-selected methodology?
the reliability of science and the contingency of the brain
If the brain is nothing more than the contingent aggregate of lifeless matter, and the mind reducible to or identical with its contingent workings, why rely on it to when it yields the result that the mind is merely such an aggregate?
the primacy of intellect or will?
Or in Matthew Arnold’s parlance, whether Hellenism or Hebraism has it right. Plato, Kreeft tells us (giving us a mild heart attack in doing so, because who else these days would claim to know exactly what Plato thought?) held rationality to be supreme, while the Biblical tradition holds love, which is an act of the will, supreme. Thomas’ response involves differentiating between types of objects. It’s better to love God than to merely know him, and it’s better to know created things than to love them. This is because in love, unlike knowledge, you conform yourself to the loved object, coming to resemble it. And so it’s better to love what is higher, and best to love what's highest.
If only for the joy of nitpicking I would question this notion of Hellenism, or at least of Plato. A host of passages in Plato's works suggest that the Forms are not merely objects of knowledge but are the proper objects of love, too. Iris Murdoch comes to mind in this regard, and the Symposium, and for that matter the Phaedrus, the Republic and so forth. The philia that you might have for a friend now applies to the highest acts of knowledge, sophia, and one consequently turns away from the love of sights and sounds. In fact it is only in the Theaetetus that knowledge gets treated antiseptically after the manner of modern epistemologists, and here only in parts — the themes of friendship and social coherence play a big role in the dialogue, too. But this is only an ancillary point.
the first way and the principle of inertia
Thomas tells us that anything in motion requires a mover, but Newton would have it otherwise. Or so it would appear: the difference is that Newton’s 'motion' only covers what Aristotle would calls 'local motion', leaving other forms of motion — increase, decrease, and alteration — unaddressed.
Here I must pause and ask the obvious question: to what extent can we reduce these latter forms of motion to local motion? I think this has everything to do with the notion of substance, viz., are “atoms” in the philosophical sense more ontologically fundamental than the things they comprise? Upon consideration, the choice for atomism does not let us off the hylemorphic hook. For any atom, be it ever so small, is extended and thus composed, and as such in need of a principle of unity (read: “form”) if we are to call it a basic unit of reality. Even a particle of Plank length would have a center and extremities (recall part 2 of Plato’s Parmenides), and thus parts, and thus a form, if it does indeed exhibit unity. And thus even such an atom is a hylomorphic substance. Edward Feser snarked up the same point recently, putting it this way:
Even if atomism or some modern variation on it were the correct account of the ordinary objects of our experience (which it most definitely is not), that would not eliminate the distinction between substantial and accidental forms, but merely relocate all substantial form to the level of the atoms (or whatever the fundamental particles turn out to be) and make of everything else in the universe mere accidental forms. The idea that modern science “refuted” the doctrine of substantial form is one of the many urban legends of modern intellectual life.
I personally would go on to say that if we perforce allow tiny things to be substances, then it would be simply prejudicial to deny substantiality to larger items. Substantial forms, not being physical, have no reason to discriminate between large and small. There's a lot more to be said here, but...
Now I suppose you could take things in the Boson-Higgs direction, say that the “atom” is not extended. But it’s still composed of genus & species, potentiality & act, being & essence. And being a composed unit, and one capable of change, it exhibits Aristotle’s non-local forms of motion in a way that cannot be adequately recast as local motion. And so, even in this case, the argument of the First Way stands.
The last recourse is to give up on atomism, and banish substantial forms by recourse to radical nominalism. There’s a beauty to this, I own. But either way you go, it is here in ontology’s very basement that this all-important decision is to be made. As above, nominalism can’t assume atoms. And moreover, I don’t think it can assume resemblances, either, even though it depends on them for survival as a theory. Given some time and gumption I shall someday rhapsodize on this…