Sakurai did create a new design for Pit, though.
Link, Zelda and Sheik are still in their TP looks, because TP was the last game to have an adult Link, an adult Zelda, Sheik and Ganondorf in the same game. (Though Sheik wasn't actually in TP, she was still designed for that game anyway.)
Sakurai is aiming for a consistent art style for the Zelda series characters, Toon Link aside. Even if the characters weren't, the Heart Container was updated to the Skyward Sword look. Plus, the Fairy Bottle has its design taken from Skyward Sword, same for the Gust Bellows, and then there's the Skyloft stage and the Beetle item, so it's not like Skyward Sword is being ignored.
Personally, I think the Zelda series is actually quite balanced when it comes to representation, as you've got items and ATs spanning older and newer games.