Edward Snowden's diss of season two of The Wire (while he's "really enjoying" the show overall, he thinks season two is "not so great") isn't by any reasonable standard one of the more important things to come out of his interview with Brian Williams. But the end of the season can be read as a critique of the war on terror — a critique that closely resembles ones Snowden himself has made.
As fans will recall (lots of spoilers to come for people who haven't seen the series yet, obviously), the main investigation in season two centered on a Greek criminal syndicate. It's run by a shadowy figure known only as "the Greek" (Bill Raymond) and his lieutenant Spiros Vondas (Paul Ben-Victor) and works with the Baltimore dockworkers' union to smuggle drugs, stolen goods, and women into the US. A police detail is formed after 13 women are found suffocated to death in one of the Greek's shipping containers, and the body of another woman from the same boat is found tossed overboard. Just when union head Frank Sobotka (Chris Bauer) is convinced to help the police take down the Greek and Vondas, the group receives a tip-off from FBI agent Kristos Koutris (Tom Mardirosian) that Sobotka has become an informant. The Greek and Vondas kill Sobotka and the case unravels from there.
The show implies that Koutris' tip-off isn't due to corruption, necessarily. Rather, the Greek himself is an informant who's helping the FBI combat terrorism, and Koutris helps him out in exchange for that assistance. FBI agent Terry Fitzhugh (Doug Olear), who's working on the docks case with the Baltimore PD, calls Koutris one of the "9/11 boys in DC…I'm guessing Vondopoulos or The Greek was an asset to them." When critic Alan Sepinwall asked show creator David Simon about Koutris, Simon told him the agent "genuinely thought The Greek was helping him nab terrorists, and if that meant looking the other way on other crimes, even warning him about impending arrest, then that was a trade-off he was willing to make to fight The War on Terror." Of course, there are legal limits to what one can do to help informants, but an inspector general's report in 2005 found that violations of those rules are very common.
While Simon makes clear in the show (and his writings elsewhere) that he views the war on drugs as a horrible and destructive waste of time and resources, the investigation into the Greek's operations isn't about drugs, ultimately. It's about getting justice for those 14 women. Maybe the tips the Greek provided the FBI prevented terrorist attacks with a greater death toll than that he himself has amassed. But I really doubt it. "Bathtub falls and police officers kill more Americans than terrorism," Snowden once noted, "yet we've been asked to sacrifice our most sacred rights for fear of falling victim to it." You can view season two of The Wire as making a closely related point: we've sacrificed our ability to pursue the people responsible for the deaths of 14 women because our federal government is overly focused on preventing terrorism. I'd think that's a critique that would resonate with Snowden.
For what it's worth, Simon appears to think terrorism is a more significant threat than Snowden does, and has been critical of Snowden and other critics of NSA surveillance, noting that metadata collection has been a staple of police departments for decades. (For why this argument may not hold up, see Conor Friedersdorf.) So he probably doesn't buy into this reading of his work. But for someone with Snowden's beliefs about the war on terror and the security state that was built to prosecute it, season two has a lot to like.
Oh, and for the record: season three > season four > season one > season two > season five.