One problem of water is unlike land the availability of resource is limited. On land with a villager you can have all the four resource (food, wood, gold and stone). Trade cart add some gold too.
Also the villager can build building unlike the fishing ship.
On water initially you can fish for food and then build fish trap for food.
Also for gold you can trade and now there is oysters.
For wood the next water rework will add trade for wood but this require that there is dock to trade.
Here some ideas to increase the resource on water in order to have the fishing ship more useful.
Food
Chinampa : an unique replacement for the fish trap for the Aztec civilization see detail here
Wood
There is already food on water with reeds and Mangrove tree. We just need to allow fishing boat to gather from those tree.
Also some other source of wood can be added : drifted wood and shipwreck.
Gold
With oyster the problem is resolved. Maybe we can expand the gold variety with trade shipwreck or red coral.
Stone
Coral was used on east african coast to build buildings. Also mud brick were used to build some building, maybe a source of clay can be added.
The problem of drop-off point
Another problem is that the villager can build drop-off point and the fishing ship no. Maybe we can resolve this problem allowing fishing ship to build docks (and shipyard in Chronicles).
Another solution can be a mobile drop off point.