There are lots of good ideas here to build upon.
I think the best way to do this would be to make fish traps work like livestock. They’d start close to empty and fill up over time, and could be stolen or gathered from if you don’t have any units protecting them. It would make it a little more APM intensive to offset the huge bonus of the extra eco.
Going along with this, I think whales should also be made finite. In reality they were hunted almost to extinction so them never going away makes little sense.
Yes please, it would be so much better for the charged attacks to be toggleable.
Good ideas, this would make them more versatile and interesting.
I really like your idea of costing population when exceeding limits, but rather than using build limits, I’d go further and make a separate naval population limit.
Each Dock built could support a ~15 naval population up to a cap of 50, and ships would have costs roughly corresponding to their current build limits. Instead of being a hard cap, any naval units above the limit would cost regular pop and eat into your limit for land armies.
Something like the population costs below would give roughly the same as the current limits. But now you’d have more flexibility and could do things like make a navy that’s entirely one type of ship. That would open the door to an actual naval counter system.
*assuming Inca gets another boat type
Boats from native allies (Canoes, Wokou Junks, Battleships, etc) could cost no pop, but have build limits.
I’m leaning towards having Fishing Boats use naval population instead of regular population even though that could be a huge buff to water ecos. However, as soon as they’re challenged, you’d be back to eating into your normal pops to build ships to defend them. You’d also need to make a few extra Docks to support the population if you didn’t want them taking up land population.
Another thing naval population could be used for is hybrid units. There could be units like Marines that cost both regular pop and naval population so that you could use the naval pop space on land too at the expense of the water.
It could be great for civ bonuses too. For example, maybe Brits have a higher naval pop limit, or Danes get naval pop space from trading posts, etc.
The native civs other than Aztecs really need a bigger selection of ship types (same for Indians). Incendiary Canoes would be a great start. I’d also add the following to their rosters:
Inca: Reed Canoe
Hauds: Cheemaun
Lakota: Bull Boat
Aztecs: Dugout Canoe (instead of regular Canoe)
More details:
Another thing I think could be relatively easy to add in would be giving Docks the ability to “portage” garrisoned units similar to Commanderies. That would let you build a Dock and get your Fishing Boats out of depleted waters cut off by shallows.