Stop-motion was starting to get interesting as a special-effects form in the early 80s, with Phil Tippett's experiments with the Go-Motion technique in E.T. and Return of the Jedi. This was when they began blending motion puppetry with stop-motion to create a more fluid effect. I think this form would still be workable now, and has influenced the work in Tim Burton's stop-motion films, as well as Aardman's output.

CG can be very effective, but artists need to understand its limitations and work within them, rather than pushing the technology to places where it clearly should not go. Pixar excels at this sort of thing with its CG animation, and it looks like Robert Zemeckis' ImageMovers collaboration with Sony Pictures Imageworks is starting to get the point with its upcoming film Monster House. Robert Rodriguez is very good at understanding the limitations of CG, and I'm sure Lucasfilm will get to that point sooner rather than later.