I think a great deal could be accomplished quite simply:
1) expand the brigade system to capital ships, so we could attach things like catapult-launched seaplanes (better search ratings), and tankers (greater range), etc.
2) give ships specific orders (sounds like this is being done) so the Bismarck can go convoy-hutning without automatically engaging every enemy surface ship in sight
3) implement Math Guy's simple system of search modifiers so that the real cat-and-mouse of the Atlantic and Pacific can come to life.
Beyond this, I don't see any crying need for changes, except that ships engaging unarmed convoys should only lose org, not strength as well - but this has been brought up at length elsewhere.
Oh, and of course the always-ongoing AI improvements.