Wind Waker allowed Link the capacity to pick up weapons wielded by enemies for the first time, but it did not permit him to keep them, while Skyward Sword, which is set at the earliest
point in the Zelda
timeline, is effectively the story of the forging of the Master Sword and thus has a sequence of swords that represent the steps
along this path (Goddess Sword, Goddess Longsword, Goddess White Sword, Master Sword, and finally True Master Sword).
We know this has been a flood of information that seems to have come out at once, but remember that we're dealing with breadcrumbs from different
points along the research and development
timeline.