I think the issue lies in that the villains were never that interesting anyway. Hector Hammond's always been something of a pushover villain in the comics, more of a cosmic joke than anything, and Parallax is just a fear entity who causes other people to do bad things or feeds on fear. The portrayal of both Hammond and Parallax in the film was terrifying and disturbing at points, even moreso than a number of other classic DC movie villains over the years, so I don't think they were bad villains, per se. They just weren't terribly interesting ones.