Smallville plots since the end of Season 2 started to be focused on Clark's fights with super powered guys or with criminals like Morgan Edge, and he's starting to see how powerful in terms of resources Lionel Luthor and his son are.
Pete was on his side, a key character, he helped Jonathan into stopping Clark when he was wearing the red kryptonite ring, plus he helped him into hiding the kryptonite in the forest, he saved Clark's life of various occasions, he was a sidekick in some way yes, but he was also his best friend.Now Clark is more focused on Lois, Lana and other characters, and Pete was becoming useless with the plots in the Season 4, Clark himself has achieved all of his powers, superstrenght, invulnerability, superspeed, x-ray vision, heat vision, hyper senses, only flight and super breath are left.So, he can solve any kind of problem on his own, except if he must face someone that possess kryptonite.He's becoming more "Superman" in the sense that he acts alone to protect his family, his friends and Smallville.