In my opinion the whole weight of the show rests on this relationship, which pushes the top/bottom concept quite hard. Jesse Pinkman is a very vulnerable character, and ‘Mister White’ is mean-to-evil in exploiting his power over his former pupil.
The first season began with the whole thing played to conventional comic effect: the buttoned up introvert intellectual thrown together with the more street smart sensualist. This conventional relationship quickly collapsed into something quite different, with the teacher becoming almost demonic and the young drug dealer more or less emotionally and physically destroyed. At the same time Jesse is drawn to Walter, and comes back to him repeatedly, and seeks a relationship with him, but gets almost no mercy. I don’t want to give spoilers, but all the things I thought Walt would never do, he more or less did to Jesse, apart from abuse him.
The first half of the first season makes you think you understand the show. It is initially positioned a bit like say Burn Notice or Dexter, with the maverick/clever guy on the margins of society, solving problems with improvisational science, the dark comedy etc.
I don’t know at what point they decided to move away from that model, and I have read that they didn’t have a precise plan at the start. I think what happened is they abandoned the ‘reset’ that you get in serial shows of this kind, and the rational arc. I think it might have been a gradual drift, or pushing, and finding that the actors and the screen writers were up to the task. I think the acting is more impressive even than Mad Men, because in MM they become beautiful in tragedy, while in BB they become ugly and evil.
I would not be surprised if in Season 3 the two characters have some sort of sexual relationship with each other. If not, I predict it for season 4. And I think in a way this would be a massive slap in the face for people like me who used to being pandered too in the most delightful way by shows like Life on Mars. It would rub our faces in how emotionally problematic and painful such a relationship would be.