It is different. The characters in Clerks were in their "College age/bummed out at not knowing what they wanna do with their life" phase, which is one thing to identify with, but the characters then grew for the second movie and therefore the dilemmas they face are more something we at our current age range have to deal with. That seemed to put some (especially the younger) folk off. Along with the less-nihilism vibe and bigger production feel.
I thought it was well worth seeing though, there is some classic stuff in there..