There is a a few things I'd like if they decide to make NPC appear organically give crews a NEMESIS this goes back to the days of CHAMPIONS ONLINE, where you were capable of creating your own nemesis.
"Making the Nemesis a "character" meant that we could give it all the tools we give our regular players -- each Nemesis gets its own costume, its own name, its own powers, its own minions, and its own back story. That also meant we had to do a significant amount of work to store and manage other full characters attached to your main character.
We also wanted to make sure that the Nemesis system fit in well with the rest of the world. We needed to integrate it with the mission system so it felt natural, not like a separate game that you played for a while before getting back to the main plotline"
It was a pretty interesting feature obviously as time has passed Shadow of Mordors has expanded on that idea and made it much more interesting.
Sea creatures would be fantastic but i would love to see them retreat and appear at RARE occassions, so it'll have battle scars from battles with others or previous battles with you..not sure how they plan to do this but i would love some sea monsters to live sort of like a good TV Series they may retreat but will return at a later season more intelligent to your tactics.
Weather I would like to see MASSIVE waves, Snowy ships with iced decks making ti slippery to stand on, dealing with hurricanes..rogue waves all sorts of MOTHER NATURE enemies.
I want to see lots of trade, livestock, breeding livestock, selling it into the market, spices - I want a Fishing pass time game...I basically want to see changes in the world.
NPC that are left unchecked for a time will eventually venture into the sea and cause you problems, sort of like the Tabula Rasa feature if you didn't do anything for awhile the enemy would grow stronger.