The biggest problem in Season 3 was Lana's amnesiac boyfriend Adam: a character so cliched that he might as well have been named Poochie The Rockin' Dog.
The biggest problem in Season 4 was that the decision to do the exact opposite of what every single fan wanted, including much, much *more* of Lana Lang despite the fact that Kristin Kreuk can't even act convincingly in a Noxema commercial. Basing a season-long "B Story" around Lana is a bad decision to start with, but making her into some reincarnation of a medieval witch was *way* over the edge.
Season 5 is much better by comparison...but only by comparison. The biggest problem so far is how the writers will spend two or three episodes setting up some interesting new situation, and then apparently panic and hit the Reset Button to achieve some magical deus ex machina
resolution in the course of single episode. For example