With a sly wink to LOST, Vince Gilligan brought the curtain down on the life and times of Walter Hartwell White, mild-mannered chemistry teacher turned ruthless drug lord; and as the camera panned upward from Walter's prostrate body, an era on television may have also come to an end. As chronicled in the book Difficult Men (Brett Martin) and extolled in print by such television critics as Alan Sepinwall and Matt Zoller Seitz, the last decade has seen a renaissance in television drama ushered in by The Sopranos and continuing with shows like Dexter, Mad Men, The Shield, The Wire, and of course, Breaking Bad.
The common thread these, and other lesser shows of the genre share is a universe of ambiguous morality, where laws are broken, good people die and the central characters are deeply flawed but written in a way that encouraged the audience to cheer for them. James Gandolfini's Tony Soprano bestrode the television screen for six seasons, with his deliberate lumber and hooded eyes, engaging in a litany of illegal and immoral activity without once losing the audience's affection or support. Michael C. Hall's Dexter Morgan was literally a serial killer, but because his victims were themselves "deserving" of their fate, we (mostly) excused his behavior. 
Concepts of "good" and "bad" in the era of "difficult men" is always a moving target in part because of the subtlety of the writing but also because the line is hard to draw. Blessed with a genius-level IQ and a cancer diagnosis, Walter White makes the rational choice to provide for his family by producing a high quality illegal drug that people with agency opt to purchase and consume. Don Draper is, to paraphrase Austin Powers, someone who men want to be and women want to be with. If he is able to ditch work for hours on end to watch movies or have sex with willing partners, should we tsk tsk his behavior because others do not have that luxury and believe in their marital vows?
Generally, our "heroes" are juxtaposed against others whose own bad behavior allows us to maintain our allegiance. Were the pushers on the corner in The Wire that much worse than the cops and politicians who stalked them? Vic Mackey engaged in all manner of illegal activity on The Shield, but he was also putting away "bad guys" and fighting some "good guys" who held high office. For much of Breaking Bad, Walter's foes were far more mendacious than him - whether it was street thugs like Tuco or Crazy-Eight or master criminals like Gus Fring or neo-Nazi Uncle Jack.
It would be easy to say that these anti-heroes are lionized - they have riches, women and the fealty of those below them, but as the era winds down, these shows have gone to great lengths to tear down the idols they so assiduously built up. The fabric of Walter White's tenuous family life was ripped asunder as the show took its bow - Walt was forced to bear witness to his own deceit - Hank being dragged into an unmarked grave, hearing his own son wishing him dead, and leaving his baby daughter in the hands of firemen after rashly kidnapping her. Walt is exiled to a purgatory of sorts, a simple cabin in the New Hampshire countryside, left alone with a barrel of money and little else but his own regret over all that he had wrought. 
On Mad Men, Don Draper was metaphorically killed during the sixth season. He lost everything - his job, his wife, and the innocence and unconditional love of his daughter. But it was not just the fact that his foundation crumbled, it was the pluck-the-wings-off-the-fly way in which it happened that made the experience so searing. Sally now despises him, but it is because she caught him, literally with his pants around his ankles, with his mistress. His wife didn't just leave him, she called his kids "screwed up" on the way out the door. And if it was not bad enough that Don was shown the door at Sterling Cooper and Partners at an early morning Thanksgiving day meeting, insult was added to injury as he bumped into former nemesis Duck Phillips wheeling his putative replacement in for an interview.
The Sopranos's controversial ending is also consistent with the "just desserts" leitmotif. Worst case, that fade to black was the Members Only hit man putting a bullet in Tony; best case, the symbolism of Tony constantly needing to watch his back suggests he will not die of natural causes at a ripe old age. Finally, Dexter Morgan's fate was also bleak. His wife was killed by a serial killer he let live, his sister died thanks to his failure to dispatch another serial killer and his son ends up being raised by yet another serial killer (!) in Argentina while he is is left to live an anonymous life as a logger in parts unknown.
In all of these scenarios, the moral universe caught up with our protagonists, justice was served, and we were reminded that bad behavior is not rewarded. Ultimately (and perhaps ironically), all these shows can be seen as conveying a deeply conservative view of the world - while spending season after season building up Tony and Don and Walt and Vic and all the rest, these shows elevated these men to great heights only to make them fall. But it appears the run of anti-heroes has come to an end. Recent series like Low Winter Sun and The Killing failed to catch on,  and others, like The Newsroom, have a protagonist whose worst vice is smoking and not being sufficiently Republican. In Game of Thrones, the bad guys are odious sadists like King Joffrey and the protagonist is a cherubic woman with an iron will; Homeland's Carrie Matheson may be crazy, but she is definitely not evil. Even critics like Soller Zeitz, who filled what could be a book writing lengthy recaps of Breaking Bad and Mad Men episodes, appears to have given up the ghost. Writing in New York magazine about CBS's remake of the late-1960s show Ironside, poo-pooed the eponymous character as "just another arrogant, angry, rule-breaking hero on the edge, as if TV needs more of those."  (emphasis mine).
1. You will get no argument from me that Dexter was a show that ran well past its expiration date. Indeed, had the show wrapped after its superlative fourth season, its stature would have been elevated. Instead, it limped along for another four, with an ending that was more whimper than bang.
2. Felina offered Walt the opportunity to set things straight - his family was taken care of financially and he gave Skylar a bargaining chip to negotiate her way out of prosecution; however, he did not survive the shoot out at the neo-Nazi compound.
3. Even so, the ending to The Killing saw Detective Sarah Linden pulling a Brad-Pitt-in-Se7en and shooting an unarmed & handcuffed suspect. Suffice to say, one assumes things won't end well for her either.