Ok, first I was kind of excited to learn that Civ5 would have "automatic" embarkation for units that have the necessary tech, but now I'm not sure if I like it.
It's maybe simpler that you don't need to build the galleys/transports yourself, but in a way I feel it takes away some epicness of the navy.
(I'm currently playing Civ IV archipelago map with Vikings, and I had a crazy invasion into zululand where I pillaged the lands and disappeared into the night with half of my invaders left dead.)
Now I'm building an even larger terror fleet, and now when I really need to build the galleys myself, it gives me the feeling that there's a grand invasion coming and I need to take time and effort to build my fleet, so when it's ready it feels more epic/important in a way.
I kinda understand that some people don't want the trouble to build the transports themselves, but for me it actually adds to the atmosphere of the game and when the coastal cities are pumping out transports they can't be building other stuff, so there's a bit more consequences too.