Wii, DS, 3DS and Wii U are all more experimental platforms than the GameCube was.
Wind Waker is great but it didn't stray that far away from the Zelda formula. Twilight Princess went back to the conventional formula. Skyward Sword, ALBW were the ones that strayed away more from typical Zelda and added more unique elements.
Wind Waker is my favourite Zelda game -- but I'm not going to pretend that Nintendo was more experimental with the GameCube than they were with the platforms afterwards.
I think the thing that is different with the Wii, Wii U, DS, and 3DS is that the hardware is intrinsically different. To look at it longitudinally Nintendo has always been experimental, but post-GameCube/GameBoy the hardware has been a driving force to being experimental (with the Wii U I think the power/HD more so than just the tablet).
When it comes to the GCN things were pretty experimental although I don't know if it's anymore of a deviation from the past than Nintendo normally does (e.g. Mario 64 was experimental) but we did get things like Mario Sunshine (which clearly continues to have influence to this point and while I'm not terribly well versed in all the background stories, it's hard not to see elements of Sunshine in Splatoon), Pikmin, Double Dash, Metroid Prime, Four Swords, F-Zero (esp w/the arcade connection), Animal Crossing (to the US at least), Wario Ware (to a home console), Donkey Konga, etc.
I will say this, Wind Waker and it's cell-shading was a BIG deal back in the day. That was a large departure and IIRC even more in contrast to expectations because of the traditional Zelda demo everyone had expected. The hardware was unique and Nintendo certainly took optional risks from a development side that weren't required, but likely part of their culture. For later generations I feel like risks/experimentation was required due to the change in hardware and the unique aspects associated with each one.
That said, the Wii U and the 3DS have largely ignored the unique aspects (gimmicks as some call them) of their system in contrast to the DS and Wii U and on the whole I feel like Nintendo's first party titles have been better this time around (although that could also be due to my state of mind approaching these games). Sure, SM3DL has unique stages, but honestly you could easily beat the game with 2D only (which some people did since until the new 3DS the 3D on the systems wasn't as stable as you'd like).