Remember that as far as the major releases go it was released in 2002 after Ocarina of Time in 1998 (and a sequel using the same engine in 2000).
People wanted a "real" Zelda game with "real" graphics, like what became Twilight Princess in 2006, whose graphics are a logical follow-up to Ocarina of Time.
It's funny how history turns out, now Wind Waker is widely lauded for its graphics, and it looks much better than the likes of Ocarina of Time or Twilight Princess.
It's a fantastic example of how Nintendo is still a company that dares to experiment, even with their most wildly successful game franchises. That hasn't always worked out, but we've gotten amazing innovative games like Wind Waker as a result.