Sakurai is making the game, not necessarily Nintendo. In this respect, it's possible that Nintendo really isn't involved in what characters are allowed in the game. In fact, Iwata might have just said something like, "Hey, if Sakurai asks you for something, you better give it to him." to all the dev houses there, and that could have been the extent of what Nintendo has actually done with Brawl. Essentially, the game's development could be in a state of whatever Sakurai says goes.
BTW, who is "The Team." Initially, it was a big ambiguous mystery we weren't supposed to know, just that Uematsu did the main theme. At that point, I wanted to say it was a division of Square-Enix, probably just from the obvious. Looking at the villains, I have to say, they look like Heartless, almost, and I wouldn't be too surprised if some of the Kingdom Hearts crew, at least some of those on art and design, were to be working on it. Any guesses now?