General ideas for re-balance+more fun.

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Just some ideas, it's a lot I know and I doubt any of them would be implemented but I was thinking about ATLAS and having a conversation with a friend and we came up with ideas on how the game could be improved.

SHIP WEAPON/COMBAT ADJUSTMENTS:
Introduce a point limit for weapons on a ship. Give each type of weapon an allotment of points.
Allow for ANY weapon to be placed on Ship, including Mortars and puckle guns. Introduce a new Mortar platform structure that is peaceable on ships that are required in order to place mortars. These structures would represent a reinforcement of the deck and should be very heavy, perhaps giving the ship a reduction in speed the same way cargo racks do. Restrict mortars to galleons and brigs only and only peaceable in the front of a ship and only facing forward (snapable to the mortar platform the way cannons are snapable to gun ports).  Adjust the point value of Mortars so that they take up a large portion of the points, perhaps half of the total amount of points allowed for brigs, and 25% of the points allowed for galleons with no more than one mortar allowable on a brig and 2 on a galleon. Remove the max crew size limit on ships. Make the ship weapon point allowance a stat that can be leveled up. (Mortars should always use up a percentage of points rather than a fixed value). The base point value of each ship should be large enough to allow for each of the available gun ports to have a medium cannon and to allow for up to 2 swivel or puckle guns per deck of the ship. Example: A brigantine would have enough points to allow for 12 medium cannons and up to 6 total puckle guns or swivel guns right out of the shipyard. Large cannons Should cost 50% more points than a medium cannon. Medium cannons and large cannons should cost more points if not placed in a gun port (50% or double) but otherwise have no restriction on placement location.

The goal of a system like this would be to allow players to have more variety in ship combat. It would also aid in sieges and help make bases that are built very high easier to siege, possibly fixing an issue that grapeshot had tried to fix with other methods. It also potentially addresses some of the issues with shotgun boats by just making the point investment of above deck cannon batteries too expensive to be practical.

INDIVIDUAL WEAPON CHANGES:

Increase the travel speed of all cannonballs fired from medium and large cannons and flatten their arc.
Increase the range of medium cannons - I suggest doubling the range but at least make them as long as large cannons are currently.
Grapeshot -  should be fired from medium cannons and not swivel guns. Range on grapeshot should be increased by 50% as should it's spread, but it's damage should scale with distance. The further you are away the less damage you take. They should take just as long as regular cannonballs to reload.
Large cannons -  should have their damage increased but their range reduced. Large cannons should have between half and 75% of the range of medium cannons but deal twice the damage of medium cannons. I know gamer logic tells us that bigger guns = bigger everything, range and damage included. However since these weapons are modeled after black powder cannons, this is not actually the case. Without getting too much into the physics of it, just know that adding more mass necessarily lowers it's muzzle velocity, and therefore range and no amount of black powder can remedy that. In order to increase both the range and the mass of projectiles, you would need to use another propellant that burns faster. In a way, nature implemented it's own "balance" IRL. 
Liquid Flame - Remove it, it's too hard to balance right and it takes away from a lot of the fun of sea battles. 
Canister shot - add a new type of canister shot that could catch things on fire, make it so it ONLY burns wooden structures and sails and only burns players who are standing directly on the burning structure.
Harpoons - Remove them. If we want to immobilize a ship we will use bar shot. As they work now harpoons are an anti-fun mechanic and i don't see a way to balance them properly. If you want to add something for ballistas to do in pvp combat, give them a flaming bolt that only burns sails/wood and they should never be good enough to eclipse using cannons as your main weapon against a ship.
Mortars - Mortars fired from a ship should do less damage to structures. This is to make up for the fact that ships can level up damage resistance and ground based structures cannot. Either reduce their damage when fired from a ship or make ground based structures take less damage than ships inherently.
Torpedos - GET.RID.OF.THEM.COMPLETELY

Remove the feat requirement to use weapons and armor up to Masterwork quality. Legendary and Mythic weapons and armor should still have feat requirements.

SAILS:

Remove current sails:
Add 2 kinds of sail, Combat sails and Voyage sails. Combat sails are fast to raise and lower and catch wind easier from a wider angle (like a mix between speed and handeling sails now). Voyage sails give bonus to speed and reduce the weight penalty to speed. If you took two identicle ships andcompared their speed with voyage and combat sails, it should be like 15% faster than combat sails if on a ship at 50% weight and the difference between the two should widen the heavier your ship. 2 identical ships at 80% weight, your voyage sails would be 20% faster and so on. This would mean that a purely combat ship would prioritize being light and maneuverable and a ship meant for long voyages could get away with extra cannonballs and cargo. In other words, having an auxiliary ship in your fleet that carries extra supplies would become almost a requirement in large scale attacks as having too much supplies on your combat ships would make them easy targets for a defending fleet.

Add a new size of sail - Huge sail Only useable on galleons. The size and point value of this sail should be such that a galleon can use 3 huge sails. Provide same speed as the 6 large sails now. Galleons just look a bit silly right now with 6 sails given that the large sails look almost undersized on the galleon. Huge sails should be a bit more proportionally correct.
The three sail shapes we have now should just be cosmetic options. Sqare-rigged sail would look like the current speed sail for example.
 

BUILDING:
Introduce a new placeable that is the ground base equivalent to the ship chest. Make it a vault or something. The vault is required in order to build anything larger than a 2 by 2 and ONLY foundations may be placed without a vault. Any structure that is built without a vault is considered a "temporary" building and it decays after 1 day regardless of player interaction. Once a structure is built that includes a vault, the vault itself has a perimeter that allows for the construction of other things. The vault works similar to how claim flags used to work in that they provide a set perimeter around your main structure that allows you to build other things. This perimeter would also disable other companies from building there just like the old claim flags used to as well. Placeables like shipyards can be placed outside this boundary, but do not count as your claimed territory, so other people can place things on or around them if they are not sufficiently close to your vault perimeter. ONLY ONE VAULT PER COMPANY PER ISLAND!!! Limit number of shipyards per company per island to 3 of each type to prevent shipyard "walls".

Peace Time - This should range from a 2 hour combat window to 24 hour combat window but should be based on the proximity of freeports and not adjustable by the company who claims it. So the closer you are to a freeport, the safer you are and the further away you are the more lawless. HOWEVER islands with lower pvp windows should be more expensive. The base upkeep cost should be both gold AND resources to pay for it. The amount and variety of resources available on the island should vary based on how far away you are as well. So zones and islands that are furthest from a freeport might be very hard to defend but have more resources and a richer variety, perhaps up to 3 different kinds of each.  Basically claimable islands and lawless islands would exist on a kind of gradient. The more lawless - the more dangerous but the more profitable. The number of completely lawless islands should remain the same as it is now and the number of claimable islands should be a shrinking gradient from there. Islands should be either lawless or claimable individually and not tied to a specific zone if possible, so one zone might have a few islands with 15 hours of pvp, one island with 20 hours of pvp and one completely lawless island. War declarations would work as they do now with two exceptions; They would require the "signature" of 2 other companies who support your declaration of war in order to go into effect. Additionally once a war declaration is made, the company who first made the war declaration also has their pvp protection turned off for the duration of the war declaration so it is more of a double edged sword.

BLUEPRINTS:

The bonuses from blueprints should be less randomized and only provide actually useful stats. No more bonuses to holding your breath or swim speed or whatever.  Bonuses should also be based on the item type. Chest and leg armor give bonus health+stam. Boots give just stamina, helmets give + health and maybe a reduction in feat cooldown. gloves could give weapon damage bonus when worn, etc.

RESOURCES:

All islands should have Iron as a base resource plus whatever types of other material appropriate to the biome. When making an alloy, rather than adding different minerals to different metals, you instead add different metals and/or minerals to Iron, which is the base metal. So Iron + coal gives you steel ingots, but then you could add other metals or possibly other minerals to those ingots to get different alloys.Right now Islands that have iron, which is the easiest to smelt, have a huge advantage over islands that use other metals. Plus it doesn't make a lot of sense to make a gun barrel out of pure silver.
Fleece should count as both a fiber and a hide.
Woods should be refine-able into thatches and thatches should be refine-able into fibers.
Salt should be extractable from sea water. If you fill a container with sea water and put it on a fire, you should get salt back and the water should disappear. Getting salt from sea water is not a strictly modern thing, people have done it for centuries.

ARMY OF THE DAMNED:
These things should be just as vulnerable to weapons of all variety as we are. Imagine having a game where you can be a pirate, you get a gun and a cutlass and grenades and the like. Then the moment you want to fight something over buried treasure the game's mechanics tells you to come back riding a bear instead. To be clear, right now you could be naked riding a level 80 bear and clear a high level treasure map, OR you could be decked out in weapons and armor and have to run away from basic soldiers of the damned because they take almost no damage from anything you can do to them on your own. On a related note, if I want to bombard soldiers of the damned with cannon fire from my ship then I should be able to do so effectively, so long as they are within range.
Ships of the damned: Just make them ghost ships.
Ghost ship: Just make it the Flying Dutchman

FREEPORTS:

Auction house - Just make an in game auction house and get rid of the individual stalls you can make.

NPC Shops - Common blue prints should be purchasable from shops and should have random bonuses rotating each day. Whatever is available should be available for purchase the whole day and not run out of stock, but should be purchasable only once by an individual to avoid hoarding of common BPs with good rolls. Different freeports should have different shops. Cannon blueprints and guns at one free port, ship planks and sails at another, etc. Common BPs should no longer drop as loot rewards.

Tames should be purchasable at shops as well but with some notable changes...

TAMES:
GET RID OF TAMING!!!
The only animals you can get should be purchased from a free port and should only be shoulder tames or beasts of burden. They can be a monkey, a bird of some variety, or a snake of some variety. The beasts of burden can be horses, donkeys or oxen. THAT.IS.IT. They give bonuses when "worn". Birds give bonuses to ranged combat feats like reducing their cooldown or by giving bonus head shot damage or something. Monkeys give bonuses to captaineering and/or piracy feats. Snakes give bonuses to melee feats. You can still level them up, but you don't tame them yourself. Honestly the more you can do to differentiate ATLAS from Ark, the better off this game will be.

STEALING SHIPS: 

If a ship is unmanned, by players or NPCs, it should be claimable within 30 minutes. If a player who owns it enters the ship, the claim fails. The feat Great Act of Piracy should reduce the duration down to 10 minutes, have a 1 hour cooldown,  and be unable to be modified by feat cooldown reduction talents or abilities. Ships anchored within the territory of their companies vault structure should be unclaimable always as should ships that have not been released from a shipyard. As always, freeports are also off limits for thievery.