The only big issue brought up is the PS3 bug. Everything else has been minor and expected for a game like this. People are just dramatic on the forums, but the wordwide acclaim this game has received speaks for itself.
There is no way in the world you can convince me that Windwaker isn't at least as complicated as OoT. And OoT was probably a little less complex than LttP, but it was their first effort to do 3D. They had up, down, and sideways to deal with and had never tried it before. But there is no way you can convince me that doing the quests in Twilight Princess and in Skyward Sword are less complex than the quests in previous Zelda games. No way.
TES games have been getting easier since they began making TES games. Each generation is more linear and involves less brain power than the previous ones. It's to the point now that I can finish Skyrim in a coma, because I don't even have to look at anything but a magic floating arrow in the sky. Keep running towards that arrow and kill anything that gets in your way, and you win.
That concept is much, much simpler than even a handheld Zelda game, which requires you to at least read the text in the game in order to figure out your next move.
No question, no contest. Skyrim may be bigger than Skyward Sword, but in no meaningful way is it more complex. No way.