I liked Napoleon Dynamite. Not because of, "hahaha Napoleon is such a dork and a loooser like every other loooser I remember from HS" but more along the lines of, "hahaha Napoleon is such a dork, but in a cyoote and humorous sort of way." I don't think the movie was meant to be an elitist way to laugh at geeks, but more of a fun way for them to laugh at themselves and laugh at HS life in general. There's also a few "geek triumphs" in that movie along with equal mocking of the "popular" crowd (Napoleon's uncle used to be the football star in HS, but look at where he is now).
As for the movie being slow at times, that's your own opinion; mine is that the consideration of that opinion is what's wrong with the direction most American movies take today. Most of the humor to me was in the monotone, delivery and actions moreover than anything else. Although, I can see why some people just simply wouldn't like the film. I think that Demi put it best (as he always does) in that the movie is really a "love or hate" film more than anything else.