The Ai will often attack the ship with the least amount of crew onboard but this is not alway's the case as they will also taregt you a lot too. In the game i'm playing i have the Black Pearl as my flag ship, the Fleut Of War and the Battle Frigate both of which have captains who's stats are not that good and can just about sail the ships but with maximum crew onboard each of them they have been more than affective at holding off the enemy who have been using ships of equal size so far,
My tactics are normally for me to focus on the big ships and tell each companion to attack the smaller ships, i'm playing as a pirate so i have a bounty on my head from France and Dutch nations. I haven't attacked many English or Spanish fleets yet because for some reason i normally bump into Dutch or French fleets and only when i'm heading back to port for repairs do i come across a Spanish or English fleet.
The area of my focus is alway's around Bermuda and over to Tortuga, its rare that i go near Charlestown or any other English towns which would explain why i see so few of them.
Playing as a pirate cargohold does mean a lot to me, i don't capture and sell the ships (household rule of mine) so the cargoholds are important to me, if i attack a ship thats carrying a lot of cargo and i can't move it to my ship i will place a officer onboard and sell the cargo at Beruda then remove the officer thus sinking the ship.
Frigates are perfect for those who like to play as the pirates, what i look for is ships with no slower then 12 knots, cargoholds of 3500 or more and crew size of at least 200. I alway's use the fastest of the ships as the flag ship any companions must have ships thats speed is at least 12 knots, but the cargohold must be around 4000+ since i like to put any cargo i have onboard the Black Pearl onboard those ships so i can continue my attacks and board ships.
I never order any of my companions to board a ship, i like them to use knipple shots for fast ships and grapeshots for slow ships, i will only tell them to use round shots if i feel the enemy could try to board them and i keep a close eye on any ships i feel might be boarded so i can quickly get there and put my ship between them.
The Black Pearl makes a perfect pirate ship because of her speed and cargohold, Frigates are good for the power and speed, there cargoholds are exceptable. Corvette's are good aswell but Frigates are better. The ship called Nightmare is one of my favourites, Constitution is a very good ship with her 56 guns and decent sized cargohold and to add to that she's fast. La Licorne, good speed, good cargohold and 52 guns (same model as Arabella). The Flying Dutchman (none quest version) just like the Black Pearl she's perfect for this role. Another good ship is the quest Corvette, Arabella, thats obvious because she's fast agile has 52 guns and can have a a lot of crew. But perhaps the best ship in the game is the quest version of the Flying Dutchman.