It fell into something that the Wire had nearly always previously avoided (the only exception being a bit in the dockworkers' arc): people felt like they were acting stupid because it was demanded by the script. Mainly McNulty's arc. The fake serial killer thing was in itself no more ludicrous than Hamsterdam, but they *sold* Hamsterdam, they sold the crazy frustration and sense of 30-years-in immunity that led Bunny to it, everyone else's reaction felt very natural. McNulty? Nope.
The second great flaw was what I call the Studio 60 syndrome: your middle aged white writer angst is way less important and weighty to everyone else than it is to you. It's possible to write a strong, tragic story about the death of a great newspaper, or even a pretty good one. This was not it, because to Simon the issue of whether Gus would be forced to take a buyout or if someone would get that job with the Post unfairly or if some writer would be forced to move to a regional office, was supposed to have the same sort of anchoring weight that the dockworkers seeing their whole world disappear did. And, um, not so much.
Third, Marlo really didn't live up to Avon or Stringer Bell as a central character. He was great in contrast; when he was going up against the Barksdales or when he was the cool young operator that Prop Joe was trying to co-op, but once all his rivals were gone he was rather dull. This only applied to a few episodes late in the season, so it was a fairly minor flaw in comparison.
But there were a lot of good points. Omar's final arc was downright Shakespearian, this great crippled lion howling out his contempt to empty streets, all his friends and companions stripped one by one; and finally taken down by an empty eyed child. I know people have called him unrealistic, but he felt larger than life in the way that some real people are. And Mike stepping into his former place also fit.
Bubbles's end was also satisfying; he was the character that seemed most certainly doomed in the first season, and his low slow road back. Yes, he got a happy ending, but it was a very simple one. Not a promise that it would be always like that, not a great triumph, but a simple meal with his family, earned hard.
Proposition Joe coming to the forefront was also nice. The supreme manipulator, the man who lived in the jungle and tamed the inhabitants, outdone by the one tiger he couldn't corral or change. Except he did change Marlo in some ways -- he made him more dangerous.
I liked Bunk, who had been somewhat of a clown if a well loved one, standing against McNulty. Yeah, Kima got the explicit takedown, but it's Bunk's furious anger at McNulty for wasting people's time, people who were doing real police work, that I remember.
Not a great season, but a pretty satisfying end.