Over on the official forums, Creative Assembly has announced that 1.4 patch for Empire: Total War will make improvements to naval battles when its released.
"There has been a re-balancing of ships to create greater diversity between different ship types along with improving the overall game play of the battles," reads the post. "The balance that now exists for naval battles is like this: Ships of the Line beat Frigates who beat Small Ships who beat Ships of the Line who beat Ships of the Line."
Basically, rock-paper-scissors element to naval battles.
"Ships of the Line are still the best at taking on other Ships of the Line. Special ships such as rocket ships, bomb ketches and galleys fill special niches on the battlefield. This new balance has been achieved by adjusting the hull strength, marksmanship (accuracy), reload rate, ranges, morale and damage of various ships.
No word yet on when to expect the latest patch, but there are loads more details about the upcoming changes through the link.