In AA50, enemy subs and transports can be completely ignored, as long as you don’t engage any of them.
(If you attack a sub/transport combo with a fighter and also try to land there amphibiously, the sub can sink your transport. You can’t pick and choose what to ignore within a single zone)
I think all the units, and particularly naval units have been handled very well in AA50. I don’t think they can add anymore units or do much better with design for this type of game.