I personally would like to see some hybrid, some ability to transport more than one land unit in a boat/ship.
In my experience with Civ3, the AI would load up a cargo ship and send it with two or three escorts to be part of an invasion. Yes, more escorts than transports. Individual little ripples (not waves, LOL) that could show up unannounced. I played less Civ4, but their AI was better about loading ships and assaulting coastal cities. While the AI could do it, I imagine that the feedback from human players was that they found using transport ships to be less fun, more busy work.
It's convenient that scouts/skirmishers and other land units can swim, I still find it hard to land a significant force and move it into battle.
Embarked/swimming units are sooo much weaker that they are easy prey for a city defender, ranged unit, or local attack ship. I prefer bringing 3 (or 4 or 5) units on a transport ship, escorted, and landing them to defend with full strength. Building a navy -- or later in the game, a carrier battle group -- was one of my favorite things to do in Civ3.