I like your heart and everything, I like that you added drawings, but.... There is not a lot of coherence to your ideas; and a lot of them are just importing more mechanics from Ark that were done away with for good reason. I don't want more Ark mechanics, I want less! (with exception to cryopods.) A bunch of this is already, or will be in the game exactly as you describe it. Like... a bunch of stuff. Especially everything to do with weather. That's already all there or will be soon.
There are some good suggestions here though.... taken on their own.
As a whole though, you are asking or a new game from the ground up.
I really really really don't like your suggestions about ship building. More classes of ships are needed, but needlessly dullifying the entire ship tree would kill the tone of the game. Atlas is comic-realism.
I think several new hulls are needed as well as expanded sail types. I too think figure heads should do more.