Hypothetical question asker! So good to have you back, it's been far too long.
The easy guess would be Russell Crowe, but honestly, I think he is just about the perfect Jack Aubrey. Brave, honest, clever as a tactician but not in the use of the English language, the movie got Jack down to a tee.
The problem was Stephen Maturin. We see him as a physician and a naturalist, but not of him as an intelligence agent. I understand cutting that part out, it could easily take up too much time, though I missed it dearly. The problem for me was Paul Bettany, far too tall and ten times over too pretty.
I was trying to think of better casting and the best I could come up with was David Bamber. My favorite roles of his are as the obsequious Mr. Collins in the BBC mini-series version of Pride and Prejudice and his turn as Cicero in HBO's Rome, who stands against Caesar on principle but is not soldier enough to stand against him on the field of battle. Mr. Collins puts him in almost the right costume, and his Cicero shows him very capable of playing a beautiful wordsmith but not a beautiful man. This haircut does an excellent job of hiding his ears, which stick out like the open doors on a 1957 Buick Special.
Of course, there is nothing like reading Patrick O'Brian, so it's just as well they made the one film to take a not particularly accurate snapshot from the twenty novel story of Aubrey and Maturin, and leave the rest of it to be enjoyed as it truly should, on the printed page.