I'm still adjusting to all the new storylines and quests, so my normal mode of play is very much a straightforward one, really. Though I am liking the looks of the other storylines so once I have a bit more time will probably go through them properly too.
The only tweaks I make are that I tend to turn rum and food off (i know, I know I'm awful) as I like to focus solely on the personal aspect. I use all the other mods though and have been getting very accustomed to using realism mode since playing Build 14. I also get notified of all sightings (makes it more unpredictable and realistic that way), and tend to play at sea dog difficulty. I havn't tried Iron man as whilst I love the concept of Direct Sail, I'm not sure I'd have the time or patience to constantly play that way!
I'll normally start on the standard storyline, as it affords the greatest freedom, and with the war tartane or even normal tartane if I'm feeling brave. I like building myself up; that's what this game's always been about for me. I'll then do some trading and absolutely completely avoid any and all at-sea engagement until at least ship tier 7. Normally this means only taking close proximity trade missions to begin with, though doing some escort missions from the taverns is normally a good way of ensuring I at least have some chance of winning a fight if I should get dragged into one! As for my character and allegiance, I'll always go as Gunner for England; mostly because this fits the storylines best and everything's in English so it just makes more sense; I have played a few campaigns as the Spanish though, as I do love some of their ships and islands!
Eventually, once I get enough money, I'll upgrade to something else; normally a Barque of some kind or a sloop if I can afford it.. At which point I'll start getting into the main quest and also having an explore to see what other quests are around.
I confess I've never played a campaign as a pirate; I'd love to though.
I know it's probably a boring mode of play this one, but it's great feeling the sense of achievement going from tartane to SOTL without needing to break the law
The only thing I'd change personally would be maybe a way of choosing an exact date, year and location in the standard storyline and maybe a few others? I don't know how possible this is due to the quests breaking but one can dream