I totally see an isometric zelda maker as a possibility. I wouldn't be surprised if Nintendo is actually considering it. Remember that was actually how the first Zelda game started.
That said, I don't think it's very likely that we will ever see a 3D zelda maker, for a long list of reasons...
Don't see it happening and it doesn't sound like it would be much fun.
I kind of agree with this, mostly cus the reason why zelda isn't "a zelda maker" is because Miyamoto realised it was more fun playing the dungeons than designing them, back in the development of the original NEZ Legend of Zelda