I've always fantasized about having two different shipyards, based on the MaxDepth tag. Sadly, it wouldn't work with existing maps, which goes against a central tenet of ZK, so it ain't gonna happen.
The two labs would be analogous to "vehicle" and "tank", but really the intent would be having a lab you can balance against land units and a second lab that just says "f*ck you, I'm a boat" and is totally OP against hovers and land units.
Basically, ship fac and boat fac.
Boats can go in any water, no matter how shallow, and have very long build-ranges ranges and a heavy emphasis on high trajectory artillery and raiders, allowing them a good ability to affect the land. They would have amphibious attack robots instead of hovers (make these bots available to Athena if you want to use them in a land game). They're units you can bring out on a "land" map that has lots of shallow rivers.
Ships are more like the current shipyard with a bit of a worse depth tolerance, and without the scout boat. The only real way to make this work on existing maps would require an engine extension - have a "slopemod" like tag for shallow depths that means that these deep-hull ships
can travel over shallower waters but move terribly slowly.