Nate Ahearn of IGN has written an article exploring the possibilities of using motion controls in NBA games for elements such as free throw shooting. The new NBA Jam will indeed use the Wii's motion controls for shooting but the article considers the possibility of using such an approach in sim-orientated titles such as NBA Live 11 and NBA 2K11. If you're interested, you can check it out here on IGN.com.
It's an interesting possibility, though I personally favour a more traditional control method. I like the idea of it being optional though, so that you could choose between using a button/analog stick or the motion controls. Indeed, I think you'd have to account for both since not everyone is going to invest in the Natal or Playstation Move.