Skyward Sword is an uneven game for sure, and the game that showed the formula they'd followed since Ocarina of Time was starting to get a bit long in the tooth, but it does so much so right that I can forgive its flaws.
That said, I feel it's less a stepping stone to BOTW and more a last holdover of its kind before its successor brought about a much needed revolution that was as much about diverging from Skyward Sword as evolving from it.