Fishing as a food source
We stranded on an empty island... if I learned something from all these stories about stranding: gathering some fruits and fetch some fish will increase your chance to survive. So, crab your fishing rod and get something for dinner :)
My suggestion: You can build a fishing dock. It will gather food from the ocean around your island. Like oil and other ressources the quantity of fish will decrease over the time, but it slowly regrows, if you use your fishing grounds wisely. Polluting the water to much will kill the fish and stop the regeneration. Getting too much fish will decrease the regeneration rate also. If the quantity reaches zero, you destroyed this source of food for a long time.
The easiest way to implement this is a building like the trading dock. It needs a number of workers to operate and will produce a random quantity of food. Maybe you can choose the number of fishermen (and fisherwomen of course).
Another (or additional) way to use fishing is the exploration map. If you explore the spots around your island, you can also find fishing grounds. A dock with a fishing vessel can go there and gather some fish. The fishing vessel needs fuel and workers to operate (like the cargo dock). Randomly the vessel can get into trouble:
Misfortune: Your vessel comes back without any fish
Storm: your fishing vessel got some damage while fishing and needs repair
Pirates: Pirates attack your fishing vessel, damaged it and stole all your fish. You need to repair your ship and need to fight against the pirates to get your fishing ground back.
How about a merge of those two ideas proposed above: a fishing dock using cargo ships pool just like cargo dock, but unlike the cargo dock, it has no spots for module attachments (has input and output ports like shipyard). The cargo ship changes entire model to fishing trawler if assigned to work for fishing dock. The dock is a food processing building (assumed it packs fish in cans) - consumes a bit of steel and produces food as trawler unloads (third input is diesel to refuel the ship). Trawler departs automatically once unloading is complete, and the catch size depends on the water pollution level (full capacity if no pollution, and the more it, the lower the cargo percentage). The fishing dock, therefore, must be a unique building, but to scale it up, it shall allow assignment of multiple cargo ships (can take more than one). The more ships assigned, the more frequent they drop by (single ship will take many game month for a single travel, so with more ships the travel time lowers)
commercial ships can be huge -- A whole new research tree. you start with a small trawler on a wooden piker, then a dockside cannery, and can progress to larger and larger pier, then concrete wharf, larger fishing trawlers, purse seiners, ocean going canning/processing ships ships. May need a frozen food warehouse on the shore, which uses the cyrogenic canisters.
I'd have to disagree with this feature. How many other games, that are colony simulators and resource management games (outside of Anno), have fishing? And in the real world, you set up farming and mining operations - not fishing. In fact, the only way they get fish is by importing it or buying it from locals (especially because they're likely going to pollute the water source near them with their byproduct). I know you addressed pollution and it affecting fishing, but it's not a good direction to go.
So where does fishing fit into this? Sure, you've got ships for oil/cargo/exploration, but I think that fishing would be the wrong direction for a game such as this. Be happy that they put farming.
expand by tech to other seafood as well?
Fishing sounds good, have it tie into the health make it an overall pool, and have range effect the health of fish the more pollution in the waters the farther your boats have to go to fish, thus more repairs and fuel usage for a trip.
As for above, All major powers fish for themselves first. Tuna is about the only fish that gets sold to the Japanese market first.
Could also be used to set up trades with smaller ports, they give you fish for X
The oceans around your island should be an excellent source of food. It would be excellent thematically and even work well with the health and pollution systems. Making seafood its own food group that gives health would represent how important iodine is and how debilitating iodine deficiency and goiter can be. Likewise, the game's theme is after a global industrial collapse so any fish shoals found during exploration would likely be small and weak, leading to hypersensitivity to the player's water pollution score. If these shoals are on the world map projects could be done (clean up polluting wrecks, create artificial reefs, setup mariculture farms) to improve their output. Conversely, oysters are filter feeders so oyster farms could offset a small amount of water pollution while providing food. All of this would help the game really play up its naval theme.
Not to mention all the food you could make with fish and other sea food, lutfisk, bacalao, and so on...
I love Mr. Coffee's suggestions. Fishing grounds as discoverable map spots makes sense, and it ties in easily with the already established mechanism of world-mines.