The only benefit I can see from Nintendo's eyes is that the sales would probably be better on 3DS. Ocarina of Time 3D sold 3.35m copies as of last March, Wind Waker HD sold 1.22m copies, though I'll concede WW had only been out half a year by that point. There was a massive jump in Wii U sales when Wind Waker was re-released, Zelda usually has that sort of clout. 3DS just makes more sense because of the bigger established audience already buying Majora's Mask 3D in droves, I suppose.
Twilight Princess is, in my opinion, the most cinematic Zelda game yet, so I do hope it skips the 3DS and eventually gets the HD remaster it deserves.