To the Devs
Atlas it's not lacking a strong theme. The Pirate Theme was strong enough to make millions from movies and even to create a successful tv show. In addition to that pirates ever since Errol Flynn or Burt Lancaster been a success on the screen. So was Atlas when it got released as Early Access as far as I know and experienced it.
And Atlas is not a Pirate Game. It flies the skull and cross bones here and there but it's far from piracy. Pirates seek a hide-out and claim islands, if at all, in silence. They don't place claim flags where ever they choose to dwell as those flags instantaneously would give away who and what you're dealing with.
Storm Punk: Harnessing lightning - now that sounds interesting. You might have watched Stardust one too many times. And what else is there to get on the water? Trapping wind in paper bags to run a wind mill at your base or maybe empty them into your sails when there's no wind at all ? I think you're losing it here and Dungeons and Dragons' fantasy is way too present in tons of games already. You had the chance to make something different and now you blow it (with the wind from the bags to put them to some use).
My ideas to the three main goals:
Get players out on the ocean [...] OK, and that's why you now added gold to building a ship? Leave alone that you four month ago announced that you CAN buy ships now with gold in addition to still being able to craft them with your own blood, sweat and tears. Too bad this didn't work out.
Make ship-to-ship combat fun [...] Now how can it be more fun and rewarding than it actually is, more loot/booty? But how? You must be totally out of your mind in case you think that players will load up their ships before they head into a battle, putting their 'wealth' at stake in a battle they don't know the outcome of? Or will there be rewards generated from thin air that screw up your trade system inflating inflation with high rewards of gold ?
Increase player recuperation [...]This sounds very nice but again the stupid gold costs for ships make it a pain again. Players might still have whatever your new design will leave them on land but the gold still needs be accumulated to purchase a new ship.
Trade System
In conjunction with what you plan on the ship's sector the trade system makes less sense more and more. As of right now ships are being build from parts the players craft. Better ships require better blueprints which need up to six different types of one resource, you know how your system works (I hope). Now that's where trade comes in handy: You can offer your wetwood in exchange for ironwood or gold to buy ironwood in case anyone feels like offering it. But what is going to happen to trades like these when you buy ready-made ships? And according to your Q&A you want to move the game more to the sea. Does that mean that armor and weapons become less important and therefore resources to craft better ones maybe are not needed anymore? What about tames? They will disappear as well as you don't need to farm resources any longer?
Claim System
Even the old system was completely useless. No idea who thought that pirates who rather live in hiding would claim an island which gives away their position to everyone who just passes by. And if you insist on this stupid idea then why not use a blimp to hover over the island? It might even harness a lightning as a side effect.
Ship Systems
That's the most bogus thing so far. Leave alone that it entails rendering trades pointless it also is one of the most unbalanced ideas you ever came up with. I'm screwed when I hit the sea with my ramming vessel and someone engages me with cannons. How balanced is that ? Specialized ships my a... !
And then there is the costs for the ships! Me as a single player might have enough time at hand to accumulate the needed gold for a primitive Schooner (or whatever ship) but the company I just sailed into has four members and hence more chances and time to get the gold for a legendary schooner. Place your bets on the outcome!
In the end this game boils down to a stupid gold grinding feast where the company having the most gold will rule