I personally was disappointed in some Nintendo first-party output on the GC, which really colors my perception of that console. I felt that Nintendo got into some awkward game design corners with the otherwise beautiful Mario Sunshine, and I really felt like they dropped the ball halfway through developing Wind Waker, as if they just stopped development on it and started giving really boring dungeons. And I'm sorry, Mario Kart Double Dash was... a big pile of meh to me even though I had 8-player LAN parties and played through the entire thing co-op with my younger brother.
There were definitely GC games I fully embrace though: Pikmin, Donkey Konga, Metroid Prime, Smash Brothers, Rogue Squadron 2 (3 just crushed my soul though...) Killer 7, Cubivore, Animal Crossing...
That said, I love the explosion of creativity the Wii inspired in Nintendo. I felt like where they'd lost a lot of spark with the GameCube, they rediscovered their pioneering spirit with the Wii. Wii Music and Wii Fit really pushed the boundaries of gaming and as a Nintendo fan I'm thankful for both games. The Mario Galaxy and Kart games also recaptured my love for those games whereas the GC had ones had worn out their welcome. I have yet to play XenoBlade and DKCR as well, so things can only get better. I do admit there were first party efforts I was still personally disappointed with, like Smash, and most notably Twilight princess.
But I think where the Wii pulls ahead dramatically for me is the third parties. I had a blast playing FPS' on the Wii: Far Cry, CoDs, Red Steel 2. I had the No More Heroes series to enjoy, and hidden motion-controlled gems like We Cheer and Godfather. There simply were and ARE more exciting, interesting, and unique third party games on the Wii, my backlog is still full of them: Silent Hill and Cursed Mountain are major holdouts in my (20-something strong) Wii backlog. And I'm EAGERLY awaiting The Last Story.
Oh, and then there's Virtual Console. That's just like... pure win right there.