It wouldn't really make sense to make them different for the sake of letting people buy both. From what I read at the last minute everybody who was testing the game said it was really awkward with the left handed thing, so at the last minute for the sake of making Link right handed in the easiest and quickest way possible they completely fliped the entire game. The bit I read said that the two versions will even have completely different players guides because they will mirror images of each other. This came from an Interview with Mayamoto or however you spell his name. It wouldn't make sense just to flip the dungeons and leave everything else the same.

Here is a link to the article:

http://www.nintendo411.com/articles/50/1/Wii-version-of-Twilight-Princess-completely-mirrored-to-make-Link-right-handed/

and here is the article:

"When Nintendo decided to change the controls of Twilight Princess to allow controller movements to swing Link's sword, it was decided that it would be too strange for gamers to be swinging their right hand in order to make Link swing his left. Thus, they decided to switch Link's sword arm and make him right handed.

What would be the best way to implement such a change so late in the development process? The most obvious choice would be to flip Link's character model, but with the rest of the game designed around Link attacking from a southpaw stance that would be sure to change the way at least some of the fights worked. No, the quickest and easiest solution was to simply mirror the entire game!

Famed game developer Shigeru Miyamoto had this to say about the decision: "Although Link is [traditionally] left-handed, at E3 we noticed people seemed to be using the right Wii controller to swing his sword. That's why we decided to make Link right-handed. The interesting thing is, on the GameCube Link is still left-handed; because of the mirror mode the game map is reversed."

It looks like the controls won't be the only difference between the Wii and GameCube versions of Twilight Princess! I can only imagine that it would be pretty disorienting to play through one of them and then go back and play through the other one. I may have to rent the GameCube version and give it a try after I finish on the Wii!"