Which is not to say that "Stargate: Atlantis" was a complete failure. The show was simply average in the end. It fell into the same rut that plagued the latter half of the original "SG-1" series. As I already said, the problems with the series were all exhibited in the fifth season as well.
The writers were constantly fighting the battle of episodic vs. serialized storytelling. They knew that the fans wanted to have several plot and character threads over the course of a season, but they never seemed to have a plan for how to make that happen. Apart from the first season, there was never a sense that the writers were planting the seeds over time to pay off in the season finale.
This inability to capitalize on the potential of a plot element was remarked upon in the wrap-up for the fourth season as well. In this case, Michael's gambit, the emergence of a new threat, and the formation of a coalition within the Pegasus Galaxy were all handled haphazardly. This lack of attention to detail led to a situation with the Wraith in the finale that literally came out of an alternate universe without any advanced foreshadowing. (Yet, somehow, many fans loved the prelude to the finale, "Vegas", which was an awful send-up of the "CSI" franchise.)
The most well-known example of sacrificing ongoing plot coherence and logical character development in favor of a mish-mosh combination of episodic and serialized elements is "The X-Files". Episodes of that series varied drastically in quality from week to week, and towards the end, the characterization of Mulder and Scully even changed from writer to writer, even as their iconic roles were reinforced.
This was precisely the case for this season of "Stargate: Atlantis". Other than the stop-start McKay/Keller relationship (which is overly criticized, usually at the expense of Jewel Staite), there just wasn't much attention given to character arcs. When supporting characters were brought in, they either fulfilled their genetic roles in the story or, when necessary for a given situation, acted far out of character. Teyla in particular was hard to reconcile. Ronon's semi-involvement in a love triangle was ridiculous.
If there was one bright spot to the season, it was the introduction of Woolsey as a capable and sympathetic commander. I wasn't sold on the idea at first, but he quickly grew on me, and turned out to be better than Carter in the fourth season. One can only hope that Woolsey makes a solid appearance in the eventual "Stargate: Atlantis" DVD film.
The fifth season of "Stargate: Atlantis" earned a Critical Myth rating of 7.2, which is just slightly above average and a slight dip from the fourth season. That is also the approximate rating for "Stargate: Atlantis" as a whole. It certainly had its moments, but too often, the writers were clearly making things up as they went along, and it never seemed to come together as well as they had hoped.