I don't quite get what you are comparing. Rally points and path finding, which by the way neither are "unrealistic", both help the player control his troops with less - pointless - clicks. I'm sorry, but the "stupid transports", as you put it, were and are an essential part of any oversea attack in history of mankind, and the logistical efforts involved in building and using them had to be taken into consideration by any given power. This is an entirely different entity than in your comparison. The player is forced to give naval invasions more thought and consideration, just as in real life, since in real life leaders couldn't just throw their troops into the ocean and watch them swim towards their enemies.
As much as I am tempted to allow you and others to believe I struggle at prince and wish I could just press a button to win automatically...
I am not the one who is having trouble with boats magically appearing at a coastline but but not at having a bridge/boat magically appear when troops cross rivers (or do they just swim across the mouth of the Amazon?) or planes magically appearing at airports ( or are their arms just tired after flying in from New York?).
But have a boat magically appear at a coastline, and good grief, that like totally boggles the mind. Especially since the thought of having a rally point for invisible transport capabilities is a radically different concept than a rally point for visible land troops.
And while we are at it SunTsu... transporting troops is EASY compared to the need to transport food and munitions for them. Does that mean we should manually shuttle boatloads of food and weapons to each stack? That is actually an enjoyable focus of a civil war game I like, but line of supply has never really been appropriate for a grand strategy game like Civilization.
This is so clearly a 'CIV 4 didn't do it this way' rant that I almost feel guilty mentioning that change can actually a good thing in the rant thread. You know kind of like steam letting me buy the game for $5 rather than $50 might actually be a good thing too.