I could discuss this movie a lot (especially since I went and read the first 4 books of the 21 book series the movie was derived from... and let me say, this is one case where the movie is better than the book or books - unless they kept improving after the first 4).
I tried reading the first book and it just turned me off. I'd already read the Hornblower books and Forester is just more readerly. The Hornblower series are a hoot. O'Brian's books feel are too showy and descriptive (to the point of making up fake nautical bull**** to make the reader feel alienated from the proceedings, but also "really there"), where Forester gives us just enough description to give us the sense of being there.
Interesting you mentioned Aubrey's superstition, as Maturin seemed to play as the antithesis (a man who embraced science and empirical evidence over superstition or religion). It was their oppositeness (is that a word?) that made them friends.
There is a divide, but Aubrey is not without his technical proficiencies. He instantaneously surmises why the Acheron is faster without giving up sturdiness when he is given a model of the ship to inspect. He can also navigate with extreme precision, which requires substantial mathematical acumen. He is also musically accomplished as is Marturin.
If Aubrey is the antithesis of anyone, it is Hornblower (the character that O'Brian "borrowed" from when he was basically commissioned to write new sea-faring adventures in the mold of Hornblower). Horatio Hornblower is profoundly tone deaf (he only hears music as noise), where Jack Aubrey is deeply musical. Hornblower hates being drunk. Aubrey loves to tie one on. Hornblower is withdrawn and introspective, where Aubrey is open, especially with Marturin. Hornblower has bad luck with naval prizes and credit in big battles, where Jack is lucky.
I'd say that the divide is that where Aubrey is a man of his time, Marturin is a man of our time. Marturin is a rationalist, scientist, empiricist, and humanist. Aubrey is a patriot, a pragmatist, and while he has shares qualities with Marturin he is a Navy man, raised on the high seas and who loves the service/life. It's kind of like night arguing with the dawn as we, the reader, find ourselves in the light of our day, trying to reconcile life in a world where men on the street might be abducted and forced to serve as able seamen. We should not forget that part of what kicked off the War of 1812 was the British capturing American seaman on merchant ships and impressing them into the British Navy. Marturin is our intermediary. He let's yell back a little bit, and this is why is a bit annoying. I don't need a modernist surrogate (or maybe I do, but I need one a bit more subtle?).
Maturin was like an amalgam of "Spock & McCoy" (Spock's logic & McCoy's annoyance at military protocol) to Aubrey's "Kirk."
Right. I think this hits the nail on the head. Where the Kirk-Spock-McCoy Holy Trinity is like the relation of Superego-Ego-Id, Aubrey/Martin is a condensation of this, and this takes inside of the man as a composite character. Aubrey is really two men in one, and this is how we get inside him, so to speak, right?