There's a thin line between poor plotting and punishment. I'm all for the latter, and have no beef with the show forcing us to watch Don at his ugliest, but season six suffered from too many inert episodes.
"Man With a Plan," where Don keeps Sylvia trapped in a hotel room for what feels like an eternity (which level of Hell is this, again?), is the prototypical example. As later episodes demonstrated, Don could be made to suffer in more interesting ways (see: the conclusion to "Favors," and the characters around him could pick at him to reveal more of themselves (see: Betty in "The Better Half"). The 50 Shades of Submission talk was not cutting it.
Season five set the bar stupidly high as far as unexpected developments (Ginsberg's holocaust story, Lane's suicide), visual storytelling (the dripping faucet at Pete's, the acid trip), and engaging stories that tapped into new moods for the series (all of "Mystery Date's" terrible dread). Season six sat too long with Don, only giving us occasional insight into great characters like Joan, Betty, and Megan. This will keep it from ranking among the show's best seasons when Mad Men draws to a close next year.