Seeing the series as, in some important respects at least, an exploration of the 'crisis in masculinity' I propose that the core conflict is not so much between 'good' Walt and 'evil' Heisenberg as between Walt and Skyler, or to put it another way, albeit rather crudely, as between patriarchy and matriarchy.
The issue is control.
When we first meet Walt he is distinctly not in control. He is running himself into the ground, working flat out at both school and the carwash, open to humiliation in both. His early promise - he is a genius of sorts as his production of blue crystal meths demonstrates - has become a story of failure. Even his son is, in some physical regards, a 'failure'. The house is Skyler's domain. All he has is the classroom and that is a thankless arena. He develops cancer. He is all but impotent as we can see from the early scene where Skyler tries to hand-start him.
Once his cancer has been diagnosed he decides to ignore the family advice to take an expensive cure. The fact that he is all but ignored in the decision about his own life at this critical point is clearly important to him. The worm turns here.
Once the worm turns and Walt breaks bad, he heads off into uncharted territory, but at least he is making the decisions. He is taking the risks, using his gifts and - all importantly - he is, as he keeps stressing, providing for his family. He has a function.
What happens as a result? In the first place his cancer goes into remission, and he is sexually potent once again, in other words he is healthy, and while none of this comes easy to him - his range of anxious expressions grows ever more intense and he is frequently in a state of terror - it gives him one last chance to assume control over his life.
But that control is restricted. When, after the separation, Skyler becomes party to at least some of his schemes, she immediately wants to take control again and, when with her, he returns to his earlier condition of subservience while bursting at the seams. She has no idea how often he has been close to death or what he has seen: she simply assumes he is incompetent. His actions have, after all, impinged on hers and her control of the immediate, which includes her own and the family's security.
Control of the immediate is the starting point. Walter had no control of the immediate before. He has established a space for it now. Each time he acts he overcomes an immediate, which is thrilling as well as desperately frightening.
Control of the long-term is a different matter. Both Skyler and Walter have some sense of the long-term but, in the meantime, there are all the immediates to deal with. In one sense though Walter's conception of the long-term is clearer, because he understands that one way or another there will be no long-term for him.
The terms matriarchy and patriarchy are both loose and mostly polemical terms, especially the latter. 99% of men have no great control over their own lives. At work they are employees, a majority of them very low grade employees. Nor are most of them bosses at home. The home is traditionally women's domain and sphere of control. Under the old dispensation women decided which domestic task to do when in their own time - the men had no such choice. The great problem for them both was that they were restricted to their particular domains.
House as seen by James Thurber
Walter and Skyler were in fairly traditional domains. Skyler had control of hers, Walter was not in control of his. His genius - his power, his control, his identity - had been stunted.
Neither Walt nor Hank, our other, developing protagonist, is truly happy in fully domestic circumstances. When confined by his injuries Hank becomes withdrawn, cold, and rude. He only starts to recover once he is back in action with the DEA.
Skyler's domain meant impotence and cancer to Walter. Not because she ever intended such a thing but because her own moral balance is predicated on Walter remaining as he is.
Heisenberg is another matter. Heisenberg may be healthier, more potent (not that he shows any interest in women) and more in control, but he is on a road that leads him - and maybe his family too - to hell.
Control is danger.
In this respect the series, though focused on the crisis in masculinity and doing a fascinating and honest job of exploring what that means, actually takes a rather feminist line.
Masculinity, in extremis, as genius, is hell.
Male control is hell.
Hank - a highly competent and, on the whole, decent version of Homer Simpson - places his energies at the service of legality and the household and is therefore salvageable.