This is a really ambitious project but it sounds awesome!
I think starting with WWII is a wise decision, there's a lot of info available about U-Boats and US Fleet Boats, and it's an era a lot of people are familiar with. Plus a lot of the systems on the boats (sonar, radar, fire control) were a lot simpler back then, so it's quicker to add them to the game.
Unfortunately things like buoyancy physics will never change and will always be a pain to simulate

The best advice I can give is to make sure your code is very modular, and to use simplified simulation models at first. That way you can start simple and plug in a more realistic function for dive physics or whatever later. How realistic are you planning to make this? Are we talking Silent Hunter level simulation or a more arcade type game?
How many people are working on this project by the way?