These are the top 3 structural issues with this update that not only I have, but that I've heard across the game socials and in game from other players as well. The prevalence of these issues being talked about makes it clear that they all need to be addressed and changes made. Bugs are intentionally excluded from this list.
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Ship Renaming Deed: Charging real money to rename a ship is disgusting. It definitely crosses a line. Cosmetics are fine, but charging real money for something that amounts to a quality of life feature is ridiculous. Remove it and make renaming a ship cost gold.
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Who is Captain?: Make it so ship milestones progress every crew member's ship of the same class (galleon, brig, sloop) if they own one in that class. The fact that it doesn't is already leading to a lot of toxicity over whose ship gets used. Everyone wants to progress their ship and only a fraction of people can with the current system, leading to a lot of division in the community. The current system is not good for game/community health and needs to change. A system also needs to be implemented to control changing captains/ships in game (while staying within the same ship class of course), especially after the captain leaves.
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Milestones: The new milestones have ridiculous requirements and aren't retroactive, which is a slap in the face to anyone that played the game before this update. The requirements should be more reasonable and even then, the overwhelming majority of players still won't have a significant number of them completed immediately. They'll still have plenty of stuff to grind for and their deeds up to this point will be taken into account and respected.
Hopefully Rare fixes these clearly glaring issues with this update quickly because many players are not happy.