His evil was more passive -- just going along -- and he did have qualms of conscience. Also, he didn't really have much to do this season (or maybe even last season, too). The show was all about Walt's fate and possible redemption, and all the Jesse actor had to do was be angry and sullen and toss around the word "b*tch" a lot, which was bound to make him boring and annoying.
He engaged in certain bad actions, but he had limits and drew a line. Basically they were involved in selling drugs to junkies and occasionally killing other bad guys.
Where he drew the line, and essentially snapped, was when Todd murdered that completely innocent kid on the bike. When Walt simply shrugged his shoulders in response, that was confirmation that he was a truly evil and wicked man.