While I enjoyed both shows, I'm really going to have to say that Firefly was by far the superior show. I think that it's kind of an unfair comparrison however. Although Firefly didn't really get a fair chance, Wonderfalls got even less of a shot at achieving what it set out to. But still, based on the epoisodes that I've seen and the other scrips that I've read, I still stand by Firefly at the better show.
Firefly really is about the characters. All this stuff happens to them, fanciful and mundane, but it's about how they all experience it and how they experience it together. Also, the show, while set in the future is still about people, about the human condition and how similar things of the future are to things of the past. The scenery may change, but people are merely people.
Wonderfalls, while witty and clever, seemed, to me at least, to operate on much less of a universal principal. It was all about the trials and tribulations of one person. Certainly it showed her affect on the people around her, and thereby the world, but to me, it felt so much less about PEOPLE and more about a person. Not to suggest that these aren't also great shows. I loved My So Called Life and other similar shows, but I think what I'm getting at is that (from my perspective) they just don't seem to have the same suggestion of life, the same impact.
Like I said though, this is from my perspective, others of you may well see things differently.