About the persisting wake, I don't actually mind that. In a way, it's good because you can actually see where you're going in 3rd person camera view.
It almost resembles a shark fin skimming the surface, too. I haven't tried it in a storm yet, but I think I know what you mean about the extra bow wave effects.
I DID, however, discover that you can sail directly underneath other ships without adverse effects. I was worried you'd start pushing them along, but that doesn't seem to happen.
One other thing I'd like to look into is the dark abyss that is 'total blackness' beneath the sea. There must be a way of changing the colour, at least, to make it more like dark blue.
Unless it's hard coded, of course, because players were never meant to see it.