There is an extra element to kudos: it gives you a vague sense of how many people are reading the story. I have a story (under Lawrence of Arabia) which has gotten well over 5000 hits but only 5 kudos. This suggests that 5000 people have come to the story by accident for some reason, and I was puzzled over why... Turned out that one of its tags, new, showed up second on the Google search results for a story by E M Forster; another could be interpreted as relating to the Sandman series by Gaiman. The first one was ok, the second one I altered. Still getting a lot of hits on it, so it was probably the first one and the story isn't being read all the way through.

I definitely prefer getting comments, but they can be misleading indicators for readers who want to choose a fic by popularity. Same story has seven comments, but all by myself and kleenexwoman because we were tweaking it here and there.