I think that the biggest problem in the nautical aspect of civ is not any lack of units but the lack of strategic objectives, i.e. there simply are too few worthwhile jobs you can do with your navy. Your land units are essential: you can't win the game, indeed you can't even survive, without having adequate land forces whereas a navy is basically a "nice to have" and necessary really only when ferrying troops and settlers across the seas.
A navy isn't _necessary_: you can win without it, and usually without too much trouble either.
This is, of course, ridiculous. Navies and sea battles have played a major role in OTL history and the control over the seas and sea routes were important. Ships were much more than just ferries carrying people.
What we need are jobs for our ships: controlling trade routes, pirating trade routes, protecting your own routes, projecting influence both cultural and political, capturing enemy vessels, raiding coasts for slaves and gold, guarding your coasts and keeping it free from foreign powers (and I mean _without_ having to build that ridiculous "Great Sea Wall Of China"), and all the other many things that ships were designed for in the first place...
Make navies useful in the game and the players will build and use them. Otherwise they are just "sugar coating".