The problem with naval transports was never the concept - but the execution. The mechanics of loading land-bound units - onto a water-bound vessel create some real headaches - you only need to see how painful that was for Total Annihilation to know it's going to be a problem.
I've seen other solutions, for example, BrewLAN has a transport that crawls up on land, unfurls it's arms to carry the units, picks them up, folds the arms back into a vertical position, and goes back into the water. Yes - it addresses some of the issues, but the entire process becomes a bumper car exercise - both on loading and unloading - and the tranport's vertical footprint is so tall, it sticks out of the water on many of the even the deepest water maps.
No - the abstraction of transport, based on the flying transports we have, is really the cleanest and most versatile solution you can get.