The Fix: Make Him The One Who Has Cancer
Walter White's raison d'etre is to cook and sell enough meth to support his family after he dies of lung cancer. But, what if he isn't in danger of dying, but his son is? Walter Jr. contracting cancer or some other terminal disease instead of his father could create a more interesting dynamic for his son without damaging the rest of the show. Walter still gets into cooking meth -- to pay for his son's medical bills -- and can still alienate his family and humanity as he descends into full-on villainy as a drug kingpin.
An underlying theme of Walt's transformation from Mr. Chips to Scarface is the rediscovery of his masculinity through cooking meth and providing for his family. This is shown all the way back in the first episode of the show when he satisfies his wife in bed after cooking meth for the first time, instead of settling for the lackluster hand-job he gets earlier in the episode. The ultimate perceived end-goal of masculinity is to ensure your genes continue to live on through your children. Walt Jr.'s sickness can parallel Walter's meth cooking, and how he is destroying his own legacy as a good man by destroying thousands of lives with his meth.