Brendan Nyhan has a good post dismissing the various "Obama decline" stories that we've seen so many of; obviously I agree, since I contributed to bashing one of those earlier this week.
That doesn't mean, as I read Matt Yglesias to be saying here and here (and if I'm misreading, I apologize in advance), that stories about how the White House and the broader administration works are necessarily useless. They're useless when they are excuses to explain something that doesn't need explaining, such as why Obama's approval ratings are lower now than they were a year ago. They're especially useless when they posit a phony explanation (e.g. that he's not "connecting") and then try to explain that phony idea by looking at the personalities of various administration poobahs.
But, yes, the way that an administration is organized can affect its success or failure (see for example the Reagan White House under James Baker compared to the Reagan White House under Donald Reagan, or the Clinton White House with Mack McLarty at CoS and other people out of place or over their heads, compared to the later Clinton White Houses with far better organization). The abilities of a cabinet secretary can affect policy. And if we're to understand what's going on (whether it's to propose changes, or to fight to preserve a helpful ally, or even just to understand for understanding's sake), we need good reporters who can figure this stuff out.
Notice, by the way, that even though the Reagan White House by all accounts was far better run in 1981-1982 than it was in 1985-1986, Reagan was quite a bit more popular in the latter period -- because the economy was better, for the most part, but also because the effects of a badly run ship sometimes take a while to surface (sorry about that metaphor). So again: "hack narratives," as Nyhan calls them, are useless, but good reporting can be quite helpful.