Never had a chance to develop a tactic really. The party Vanaran monk climbed the enemy ship's mast to get a better view of the combat when he encountered her along the yardarm. She 5-foot stepped in and attacked. The monk deflected with crane wing, countered with crane riposte, tripped her with Improved Trip, kicked her twice more with Greater Trip and Vicious Stomp. Since she had only made one attack, she used her move action to stand up which got her punched in the face. On the monk's turn, he bull rushed her off the yardarm, causing her to fall 60 feet, landing on the deck prone. He used his move action to swing down after her, landing deftly next to her.
Seeing that most of her crew had been swept away by the other PCs, she took the total defense action and successfully stood up on her turn, taking only one minor hit from one the PCs. The monk tripped her again on his turn and the entire party got AoOs against her from Greater Trip, then the monk got another from Vicious Stomp.
It was horrible what they did to her after that.
So...the problem here, other than nasty....story and/or logic requirements (eewww)...is that a Fighter BBEG really serves a different role than a Fighter would in a PC party. I'm not intending to specifically accuse you, RD, of not knowing how to build a fighter BBEG btw. It is, nonetheless, a fairly common problem I've found. (Even amongst PFS writers, sadly enough). In a PC party, the fighter is usually a tank. They stand in front of the more vulnerable characters and beat things. A BBEG fighter on the other hand is actually a glass cannon. The PCs will normally have many tricks that will just shut down a fighter - will save spells, even a simple grease on their weapon.
The trick to making an effective Fighter BBEG in my opinion is to be sneaky. Hide amongst the minions and make someone else look like the real threat. Fight in locations where the BBEG cannot effectively be targeted at range - such as a smoke(stick)-filled room or behind a twist in the corridor. Have a support minion hide behind a tapestry in the throne room and concentrate on maintaining the illusion of a imposing figure on the throne while the BBEG tries to blend in with guard-minions. Use potions of invisibility, glamered armor, hats of disguise, or simply the Disguise skill. Find ways to ambush the vulnerable PCs from the rear - behind the party tanks.