Since this is about Transportation and it's in the Future Zelda section, I'd like to discuss if there could be transportation in the new Minish Cap game. Considering that Link is very small, probably insects could be his way of transportation. He'd pilot on a dragonfly for the skys, ride a mouse on the ground, and maybe a ride on a very small sea turtle to dive into the water. These are just ideas.
As for the Link in Zelda2005, I'd have to say that he's going to stay with a horse in 3D Zelda games. It just seems to me that all the 3D games are more mature than the ones on the Gameboys. And like someone mentioned earlier, Zelda is sorta taken place in medi-eval times, so the closest thing I could see Link having is a hawk (yes trained hawks were used during this time). It all depends if Link's hawk is going to be an overgrown hawk that he can ride on/attack with, or a normal sized hawk where he could use it to stun enemies/scout ahead (like the seaguls in
tWW).