You can always ignore the ruler. The only thing you get from him is ranks, and those are not required for the story. Ranks get you better discounts at the market (only), not even better at the shipyard. They may make it easier to recruit certain mates, but the seems to be based more on levels than rank.
To avoid the story, all you need to do is avoid raising the type of fame that your character's story is based on. If you want to be a pirate that will avoid the story for all but Otto and Catalina. Since their story is based on piracy fame, increasing that will advance their story (not to mention that Catalina begins by betraying her country).
Pietro can freely change countries without affecting his story. He is also my favorite character. His story is based on adventure fame. His battle stats are a little low to begin with, but they will increase fast if you start by attacking smaller fleets.
Yeah, except for the two big names (Idin and Khayr) most pirates will hide in port if you are anywhere nearby. They only leave port if you are too far to see them do so, and most of them have a set route that takes exactly one day. If you defeat Idin and Khayr often enough they may be replaced. The bad thing about that is that most of the pirates that replace them are lower levels and won't give you as much experience for defeating them.
Betraying your country can make for some interesting twists, but in most cases you can't finish the game (without cheats at least). If it's just a matter of wanting to pirate...you can do that with any character and avoid the story by controlling your fame (that's a lot easier than you might think). If it's a matter of wanting to play a different country then Pietro and Catalina make that easy. If it's a matter of wanting to get away from the story, just watch your character's fame type.
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