This show originally centered on the CIA, with Annie Walker as a lead character. By the time season 5 aired, the show centered on Annie Walker with the CIA as a background character. That's its mistake.
In other words, IMHO, the audience tuned into, and was happy to watch a good show about the CIA taking action on national issues. But during season 5, only personal issues were acted on... i.e., the CIA office being attacked, and Belenko's vendetta against Augie. That's ALL season 5 focused on. Doing so forced the greater capability of the CIA into the wallpaper.
If the writers were to bring the focus BACK TO THE CIA and highlight their capability to address NATIONAL concerns, then I think the audience would return. Watching the team work on national threats was far more interesting than watching Annie and her boyfriend spend an entire season saving Augie from a thug.
While there's something to that, the ratings were falling ever since season one, as many have pointed out.
There's a major problem with your suggestion--the CIA isn't really that popular nowadays. For rather obvious reasons. The show tried to walk that tightrope between praising them for the necessary work they do, and showing the dark side--Annie was there in the middle, trying to be effective and retain her ideals. I think after a while they just figured they'd played that angle out, and all they had left was the personal relationships that really were the core of the show's popularity, such as it was.
You know, it isn't necessary to blame anybody. It was an okay show, at its very best--nothing more. I only watched on and off because I like Piper Perabo. I never took it seriously as an analysis of the CIA, because it never remotely resembled the reality of that organization. The kind of show you're talking about would definitely be worth watching--but Covert Affairs was never going to be that show, and just the name of the show alone makes that clear. To somebody with a brain.
Oh, I didn't realize the ratings had been on a steady decline since the beginning. I actually went to the show's web page only to look up a song and that's where I caught a link to a story reporting that it was due to the significant drop in ratings only for Season 5, that they decided to cancel the show.
And of course everyone knows that the CIA wasn't the "real" CIA, simply because it couldn't have been. But that's besides the point. Early on, it was still about the CIA and the agency's exploits. Yes, made up for TV - I don't think that was lost on anyone - but the focus was at an organizational level, not a personal one. Storylines that focus on the personal always seem to paint themselves into a narrow corner.
I would say Homeland is closer to the "real" CIA as an entity, but even that is pretty far off the mark. Its consistent looking in model but the writers don't seem to take verisimilitude as seriously as the cast and crew do which ends up making them saying and doing hilariously wrong things with absolute conviction.
Covert Affairs seemed to address a few behind the scenes scenarios in season 2 but it was always hidden under layers of 'tongue and cheek' quirk. When they abandoned the procedural format later, they stopped telling the story limited to its CIA confines so it focused on the plot not the setting and went their own way.
~~~~~ What changes can be made if there is nothing left standing in the wake of rage?
The ratings drop in S5 was the reason for the show's cancellation--but the ratings had been falling before then. Once a show makes it through the second season, the ratings have to go way down before the network will pull the plug--and since it reached the fifth season, they could say with complete honesty that they'd done well by the show and its producers. 75 episodes is quite enough for syndication, though I doubt it's got much of a future there.
I think it was always mainly about Annie and people Annie worked with. And it was more about personal relationships than politics. I agree they tried to show some of the realities of espionage, but so prettied up as to undermine that attempt.
ALL shows are about the personal, and they all paint themselves into a corner, sooner or later. It's just a matter of degree.
I think if they'd done what you think they should have done, the show would probably still be canceled.