I have a few ideas for the future. Might have already been discussed:
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Armadas - a limited amount of ships (maybe max 3-5) that can sign a contract (maybe pony up some gold too) to be in an Armada. Friendly fire would be off between crews. Accords would have to be broken and contract dissolved to remove oneself from the Armada. Maybe lose some of their initial gold investment and/or not be able to join another Armada for an amount of time, etc. if a crew leaves without a consensus to dissolve. Kind of like small guilds.
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Pirate hideouts - I'm definitely sure people have discussed. This would be in line with a small guild sharing an island/base that isn't on the map. Just for them. Maybe somewhere to stockpile supplies. Place decorations. Plan their next voyage, etc. Maybe even implement a pirate king that gets more permissions than others, etc. Rank-up system, etc.
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Spyglass - 'nuff said
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Grappling hook and rope - 'nuff said
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Those small canons on the rail that shoot smaller shot. Maybe an upgrade. - ah they are called swivel guns
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Rams on the front of the ships - upgrade
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Decorative figureheads as well! Maybe some semi-risque, just a bit. Call me a perv but it's very piratey.
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Scars! Tattoos! Piercings! Stuff!
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More instruments! Small flute, shepherds pipes, hand drum, lute, etc. More songs! Maybe a system where one person could start a song with one instrument, then others join in to the same song and it fills the song out with all of the instruments being used. Would be pretty sweet.
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Ropes to swing from the crows nest to the deck or other ships!
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Maybe an extra NPC crewman that will attack enemy players who board your ship. Making the odds against the attackers. Home court advantage, etc. Would provide a bit more variety in pvp confrontations.
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Crossbows, pikes, marlin spikes, ballistae, etc. More personal weapons and more ship weapons and upgrades. All doing the same amount of damage. Just more fun to have a variety. Maybe implement specific types of damage to the ship, but this might be too complicated and messy. (i.e. take out their mast with chain-shot and they'd have to repair - need for more than just boards. Need a log or 2, etc.) Just spit-balling.
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Possible crafting addition. Mine up/collect metal ore. Smelt. Craft things like iron protective surfaces for your hull. Not protected from canons, just maybe from running into rocks, etc. Gives the ship a little more longevity, but has to be worked for.
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Fire hazards. Sails can catch fire. Would have to keep extra sailcloth around, etc. If the sails burn, maybe leave the crew 1 sail that would make them slow, but could still get back to port if they are out of sailcloth.
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More types of food. Possible add a kitchen to the ship where simple foods could be prepared. Need to gather ingredients. Simple buffs like speed +1, farseeing, swim speed, can drink more grog before becoming drunk, etc. - then seasickness can be a thing, lol. Hey there's already chickens and pigs ready to be turned into delicious entrees. Maybe even barnacles that build up on the hull that can be scraped off and cooked. Diving for clams, lobsters, etc.
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Water pump - upgrade. Can pump water out of the ship from the lower deck without going up and down the stairs. Would take time. Would have to get an achievement/work for this. Mostly just a convenience thing, but as the game progresses it could allow for more time to do other, more complex things. (not complaining, just a thought on progression)
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Mini-games: (already been discussed, but here's my thoughts) blackjack, darts (could be interesting during a storm, if hit crewmates they take damage, ec.), shoot the shark (timed mini-game where crew members try to shoot sharks from on deck. i know kinda cruel shrug), diving from the yard arms (each crewmember dives off the yard arms and the others rate their dive. whoever wins gets something silly, or maybe 1 gold from each other person, etc.), hide and seek (protected from pvp for limited period of time, ex. 5 minutes. can't start a game when enemies are near to avoid trolls), grog pong (i know, might be lame but easy to implement. 2 on 2 within your crew or challenge other crews)