My apologies for being away for so long. Stupid day job!
Well, wouldn't it be easier in that case to simply allow for movement paths to automatically encompass transports, rather than create a whole new way of getting units from A to B?
Easier? Sure. If that's the solution they use, I'm all for it. However, let me tell you what the real differences are between these Ferries I'm suggesting and the Transports in the game.
IRL, the overwhelming majority of ferries are NOT ocean-going ships. That would be a huge waste of resources to build them that way. Ferries are small, cheap, special-purpose vehicles, while transports are not. So from a reality perspective, in game they work a lot better if they're cheap workboats in disguise than if they're expensive Galleons.
Seems like overkill to make a special unit just to accomplish a small task that comes up only every once in a while. Kind of like Wineries, Whaling Boats, Forts, Obelisks (well, any Unique Building or Unit), Settlers, SDI, Privateers, etc. There are PLENTY of things in Civ4 that have very limited use. Almost every day, someone starts a post about the worst unit, or the worst building, or the worst whatever, and it's about something that player can't find a use for. Inevitably, the thread gets deluged with people defending that particular thing. Heck, I built a whole strategy around NOT building roads (and NOT researching The Wheel for about half the early game) just to see if it could be done. (It can.)
So if you're going to argue from a "What's the point of some little tidbit?" stance, consider yourself having been saved the trouble.
Maybe your empire isn't split by one tile of water too often. But some times it will be more then one tile too. I think that the ferries should be possible to be lined up, making a road of them, for example along the coast. I don´t think the ferry will be useful very often, but in some scenarios it will save you from a lot of micro management, and I don´t think it will be too powerful as long as you need cultural control of it to use it and you lose your movement when leaving your line of ferries.
Yes. There are some people who play exclusively on Pangaea and will not have a use for a Ferry very often, but there are also people who play on Archipelago all the time and who might reap huge benefits from it. Those who play on Earth maps will definitely see the value, as that's where I had the need for it pounded into me.
There is a reason why you cannot bridge a gap without a turn wait. If you could, invasions would be much easier. You would not only be able to attack coastal cities on your first turn of war, for example, you would also be able to attack cities two tile in from the coast, with tanks, modern armor and mech infantry immediately going onto the shores and pushing into enemy land. This would mitigate the vital defensive turn by the invadee (?) that is crucial for them to successfully defend their land. So this idea would only throw the game further into the hands of the attacker, which isn't really a good thing.
Tell that to the people who declare war, and then unload a dozen transports on all the coastal cities all at once, all before the defenders have any chance at all of defending. I covered my personal distaste for this exploit in a different suggestion thread about requiring a delay between DoW and invasion under penalty of diplomatic penalty in my
Penalty for Surprise Attack thread.
On top of that, the Cultural border isn't perfect, and I've had plenty of games where my border reaches someone else's city and I can sit right next to it, declare war, and take a city or two on the turn of the declaration. In either case, these surprise attacks almost always result in a vassal the very next turn. As you say, the game is too far in the hands of the attacker already.
As OP says, you can only use Ferries if they're in friendly territory. You can't use them if they're in enemy lands, or if they're in unowned lands. I think treating a Ferry like a Road is enough of a slowdown. If you insist on a one-turn delay, then why even have Ferries? Transports already do that, and as you noted above, all that's needed is for a boat to have a Ferry-mode that allows your auto-move commands to not get ruined by boarding.
I hope this has been of help. I'll post a reiteration of my idea next for those who are a little confused and want to be more so, and then I'll go into one last comment that was made and examine it.
Reiteration of the Ferry Idea
The point of Ferries is to save on some needless micromanagement. A real-life ferry is cheap, generally stays in one area over its lifetime, is not ocean-going, is not capable of defending itself from attack, and is not capable of conducting amphibious assaults. By basing Ferries off of Workboats - that is, a Workboat gets converted to a Ferry just like it can be converted to Fishing, Whaling, or Crabbing boats - we have a cheap way to build a tile improvement.
* Ferries are cheap, transports are not. In-game, Workboats are cheap and transport vessels are not.
* Ferries stay put on the coast, transports cross oceans. Ferries are only buildable on coastal squares - if you want trans-oceanic transport, it's much cheaper and faster to build a Galleon or Transport. If you have a 2-tile coast to cross, use 2 Ferries. It's a tile improvement, not a unit.
* Ferries can't defend themselves, transports can. Small boat like Ferries don't have room for guns and stuff. If someone comes along and attacks them, they're done for, no fight, they're just gone. Since these things could potentially be available very early in the game, as soon as Galleys are, it makes no sense to give them even a

of 1, because then Galleys still might lose. So just make them a tile improvement, which can be pillaged, but with the special condition that if a land unit is on that tile, it dies. Shouldn't've moved your guy there with enemy fleets around! If you want a defensible Ferry, either build a transport or station a warship there.
* Ferries are not invasion craft. Let's face it: there's things going on on the map that are too small to be depicted. When your troops are not allowed to use enemy roads, it's because they have to fight their way through. Same deal here: you can't use an enemy-controlled Ferry, and you can't use a Ferry to cross a hostile border. That's what transports are for.
Okay, now for one final comment and a new idea.
You could have another option on transport to "ferry" rather than having to build an improvement.
But I would like to do more things with the sea via improvements.
So ferries could produce gold.
You could have seaweed collection producing hammers until industrialisation
Pleasure beach producing gold and happiness - If you had six you could build the "Bondi Beach wonder"
etc
Let me thank you right quick for "getting it" and helping these guys understand what's going on while I'm not able to be here as much as I used to be.
So, what if Ferries were able to charge money for their use, or have some other benefit besides simply bridging landmasses (or cutting across bays)?
The first thought I had was that someone using a Ferry would pay a

for the pleasure. But that would practically never happen! And to make it useful, you'd have to be able to build and use them pretty much anywhere. Plop a ferry down in your opponents' back yards and hope he uses them instead of building his own? Would require ownership of a tile improvement to be different than the ownership of the tile, among other problems. It might be easier to have a Ferry unit.
Then I thought of it being something that would generate

if it was in a city radius, but that's rife for abuse potential. One or two, okay, but not a bunch.
Then I thought that maybe if the Ferry was used to link continents, there would be some sort of bonus to your income that way, but really, that would require a much different economic model for Civ, something we'd have to wait for Civ5 for. Ferries, as I've described them, could be implemented right now by some intrepid modder with a few hours on his hands and unlimited fame on his mind.
So it all boils down to using Ferries just to bridge small water gaps and pretty much nothing else. Sorry it's not exciting, but at least it's simple and practical.