OoT 3D used the same engine with improved graphics. It's an enhanced port, which is why it still has many of the same glitches. The same goes for Wind Waker HD. If you're you're denying that those are ports, then you don't know what a port is.
And it seems clear to me that X/Y is using an enhanced version of the engine. This doesn't look like it was build from the ground up at all.
EDIT: It's not the textures that bother me, but rather the lines between textures in some areas. Admittedly, it is improved a lot in some recent shots.