My opinion for rivers, canals, and tunnels missing is... flat out lack of interest to expand the boundaries of the game. Everyone can say balance. It is balance as long as we need to play the same simply civilization game.
This is one of the biggest reasons I am shying away from buying Civ5. I feel like I am getting a jazzier version of the same game. The challenge would be to balance these new features into the game.
I am probably one of only a few here, but I don't see the big upgrade to the game. I mean adding a hex grid I feel is more of something very basic. But again one man's wonder is another man's doll house.
Edit: What I would like to see would be the ability to mod the rivers so I can have them act as roads at the least. As in actually transporting units on them. I mean the majority of beginning civilizations were founded along rivers because of the ease of transportation, drinking water, sewage, and etc.
If that was possible then I would jump to the game. I have my doubts that will happen though. It is more about not limiting the possibilities of altering the map to me.
Firaxis made the coding engine so it would be legal for them to release the whole game engine