The key to a proper implementation of a navy is to make them a support class, NOT a direct attack. We have enough direct attack as it is. And realistically, that's what the Navy has shifted towards in modern times.
Like what's already been suggested, the Navy must increase the speed, accuracy, and efficiency of the military. Ideas such as raising the aircraft cap, allowing extra cruise missile attacks, and improved intelligence gathering are all excellent examples. And even then, these are all simple enhancements, there are many more possibilities.
But allowing the Navy to improve or add twists to prexisting elements, it'll make the game a lot more interesting than if we were to simply tack on yet another attack option.
There should definitely be a cap to the number of ships you can create. Otherwise, the Navy system will inevitably become "boring." The most powerful nations won't have to worry about customizing their navy, they simply buy everything and get all the benefits. The key is to make the navy as customizable as possible from nation to nation, allowing players to choose their benefits to suit their playing style.