One of popular misconceptions regarding the drug trade (and one that is fed by the term "cartel") is that the the biggest groups are hierarchical organizations with militaristic chains of command. Obviously, Chapo has more power to boss people around than some mule in Nogales, but the extent to which he has control over everyone in his zone of influence. And Chapo's seems to be the most coherent of the bunch. There has been a lot of evidence of that in recent weeks: We learned that Martín Omar Estrada was kidnapping and killing scores of bus passengers against the instructions of his Zeta superiors; that a couple bosses in La Gente Nueva were evidently disobeying orders from Sinaloa and fighting other groups linked to Chapo and Ismael Zambada in Durango; and that someone in Guasave, Sinaloa --which should in theory be under the control of Chapo's Sinaloa cartel-- had posted a couple of narcomantas taunting Chapo after having killed seven of his underlings.
As far as what this means in combating the drug trade, I'd say that it's important to recognize that the kingpin strategy is not only insufficient (though taking down kingpins has to be within the capability of authorities), but it's also very hard to predict exactly what impact arresting or killing a capo will have, because we often don't have a very good idea of their level of control even within their own organizations. I also think this is further evidence of the impossibility of an industry-wide pact with the government.