I've set the morale of all vessels to 40 now, and it seems to increase the toughness of each fight, as you've already pointed out, more casualties on each side and thus more realistic.
The enemy still bugger off quite fast (as far as the number of remaining enemy ships indicates, anyway) but it seems like the battles "last longer", if that can be said about auto-resolved battles.

I don't want every naval battle to be a back-against-the-wall, die hard battle with total annihilation of one side as the common result, but at least sinking a vessel or two in a battle would be nice.