I have great affection for traditional cell animation, but when it's done right, I can enjoy CGI as much, if not occasionally more. Pixar's really done well in this area; looking at Toy Story, The Incredible or Up, I don't think I can say they'd be better in 2D. Indeed, I think part of their charm is their unique animation style.
On the other hand, there's just something about traditional animation that makes me prefer it. I guess it just seems more alive, somehow.