SMB 3 is definitely my favorite, that was the question after all, wasn't it? It was the first video game that I ever seriously played and it was certainly the first one that I ever beat. I didn't have access to an SNES, so I wasn't able to get my hands on SMW until I was about 13. By that time, the sentimental value of SMB3 had already pushed it way high on my "favorite" game list.
Now, which game is better? I'm not sure. There are some great elements to each game, but what does one weigh as most important, innovation, perfection, controls? SMB3 brought the flight element into a Mario game in such a cool way. SMW took a more traditional flying approach with the cape, and I always thought that the cape was super lame compared to all the other ways Mario has taken flight (Tanooki Suit, Leaf, Wing Cap, etc.). On the other hand, I really enjoy SMW's music, possibly even more so than SMB3. I'm probably not qualified to decide what game is better, but those are some of my thoughts.