Yeah, fleets in MTW are all barque but no bite. I believe nobody mentioned the "splitting up of fleets" feature either.

Thus: splitting up of fleets.

If you want to sink a single enemy ship, concentrate two or more of your own ships in the same sea and preferably in all seas adjacent to it (since these are his possible escape routes). Split your fleet into separate ships and give them all the order to attack. Even if the enemy is a dromon and yours are slower barques and caravels you still have a chance of catching him. If the enemy commander has 3 stars or more, even this won't work as long as he keeps moving his dromon about. Not much you can do then. Have a good cry. Take a balloon trip around Mexico. Consult a voodoo priest. Whatever.