I prefer left handed Link, and I also noticed that on the WiiU demo, it also bothered me because on the demo the player was using the WiiU controller, not a wiimote, so I see no reason to put a right handed Link on a game that uses button and an annalog stick...
I am right handed, but I also find it unfair not to make a left hand option for the game. There are other games that give this option like wii sport resort and such ( I don't really like those games, so I haven't really played them, but I'm preety sure they do have that option).
I just find it nice the fact that Link is a lefty, and seeing him holding the sword on his right hand doesn't look right for me either... Sure there are other things that affect more of the game, but it does bother me, and the fact that they make the game only for right handed people seems like Nintendo is being a little lazy....
About the Master Quest on OoT3DS (which I haven't played btw) I don't understand why make him right handed there either. Is the 3DS Master Quest just a mirrored version of the game? Kinda like Mirror cup on Mario Kart? If so, why did they do that? Why not put the GC Master Quest with uptaded graphics? ANd why flip Link's model with the rest of the game?