Anyone here actually bother to read the Iwata Asks interview. Some part of the interview seem to imply that it is, in fact, a remake.
"Iwata: Three designers? Considering the deadline, even though it was a remake, correcting each bit of data by hand would be impossible."
"Dohta: Yeah. As a matter of fact, we found out bugs were the cause of how some of those graphics appeared on screen. So, including those things…
Iwata: You recreated them?
Dohta:Yes. I thought, “What in the world am I doing?”
Iwata: I see. When working on the shading, you even recreated the bugs!
Everyone:(laughs)"
"Dohta: The way we did it this time, even the designers making the data weren’t able to imagine how it would look when the images first appeared. Because a method had been put in place to completely replace the images, I think there were times when the designers saw those images come up for the first time and they’d be like, “What?!” (to Arimoto-san) Right? "
"Iwata: Dohta-san, you never imagined that 11 years later you’d be analyzing and reshaping the data of a game you enjoyed before you were a developer. "
I seems to me that they did quite a bit with the code
http://iwataasks.nintendo.com/interviews/#/wiiu/wind-waker/0/3
http://iwataasks.nintendo.com/interviews/#/wiiu/wind-waker/0/4