Oh and the idea that the sea units are able to "conjure ships from thin air" is an argument I don't buy. This is like saying that Archers conjure unlimited arrows and tanks conjure shells, or that Settlers conjure cities out of thin air. Where do the workers get their mining picks, hos and materials for working the land? Well it is magic?
Well, simple answer is that just because we can't see it, doesn't mean it isn't there. A contingent of troops is likely to be carrying more than what we just see there on their avatars. Food, water, supply and communication lines, equipment for salvaging available materials (axes etc.) would most likely be used on every unit. Well why don't we see it? Because it is a representation. No one wants to be forced to manage all your units' supply lines nor do we want to be responsible for equipping every unit of soldiers with a hundred and fifty little boats. We assume the boats are representations.
Here let me help you...
I have a unit of Spearmen that I want to ferry over the choke point my opponent has set up. I plan on landing on my opponents source of Iron, pillage it, and fortifying on top of it so he can't retake it. Never mind how I knock down an iron mine and fortify myself in trenches and makeshift walls when I have nothing but the armor on my back and spears, holding off for years with no supply line or food...
First, my Spearmen need boats. Do the Spearmen assemble their own boats from the surrounding trees, settlements or commandeered trade vessels passing by? This is indeed possible. While I am crossing the channel do the Spearmen hitch a ride in the decks and lifeboats of my Galley unit that I am using to protect it while they are embarked? Also possible.
Try to use your imagination here. This is a game for fun and to represent your own history. I have made up multitudes of stories to accompany my games of Civilization and they are never anything so boring as "I had three units of spearmen and he had 3 axemen and through some miracle, my spearmen survived his assault and i kept the city." They are awesome stories like "I was vastly outnumbered and my ramshackle group of Spearmen managed to sneak through a secret passage around the back of the Axemen, surrounding them and with special forked spears, were able to abuse the Terrain and vanquish them."
Now in the game of Civ, I built no underground passage, I was on the defense, and I certainly had no special spears... But that is what representation and imagination are for.
My stories in Civ5 are going to be things like:
"A Hoplite Unit, who's homes and families had been burned by the Romans in the capture of Corinth, defied all orders from their commanders. Seeking revenge for their loss, they ransacked a town of locals and built a small fleet of boats to cross the channel. Weathering tier way through a terrible storm that protected them from the Roman Ships, they made their way to the Roman Coast, where they disembarked, stealing large amounts of food and slaves from a local settlement. They worked their way into a small mountain pass, where they found an Iron Mining town that was responsible for equipping the majority of the Roman Legion Forces. Ransacking the town, the soldiers were able to build improvised walls out of the walls of pillaged houses and raw iron ore, fortifying their position. They sent raids out at night to gain food from surrounding farmlands. A single man was sent back on a little ship to send word to Athens to send reinforcements and aid, and soon enough, a unit of Galleys arrived with food, fresh water and supplies that allowed them to defend themselves against the never ending hail of roman Arrows. Without their main source of Iron, the Roman Legions on the front lines began to ran out of reinforcements and supplies and eventually crumbled to the might of Greece... all because a small group of Corinthian Spearman took matters into their own hands."
How did this go in game?
I embarked a Hoplite over the channel. It was not intercepted by the Roman Galley. It landed on the Iron, pillaged and fortified on position. Archers began to fire on it from 2 tiles away, so I sent a Galley to bombard the Archer from the sea and eventually reinforced it with an additional Hoplite. Without that iron, Rome could no longer build Legions and I was able to Rome back and retake Corinth.
I know what I prefer... although maybe I am just odd...