There are several major reasons for this:
-The Wii is in its twilight years. It's still selling very well, but at this point it has been out for 5 years. The demand for a major Zelda title simply isn't as high, and software sales for the system are down.
-At the same time, the 3DS is rising rapidly. Not only are its hardware sales massive, but its top titles (in this case the two Mario games and Zelda) are being pushed heavily.
-OoT 3D has had a very popular and well stocked bundle with the 3DS.
-The Ocarina of Time remake was really the first major title for the 3DS. Prior to that there wasn't really any system sellers in the lineup. The Wii's biggest sellers have come and gone and Skyward Sword is really only selling to the existing Wii userbase. Much like how PS2 titles started to sell less in 2005 and 2006, the Wii userbase isn't as energized.
