If its legal is still an open question imo. This is the case the article refers to.

http://www.freerepublic.com/focus/f-news/1630900/posts

This case presents the question whether the installation and use of a pen register 1 constitutes a "search" within the meaning of the Fourth Amendment, 2 made applicable to the States through the Fourteenth Amendment. Mapp v. Ohio, 367 U.S. 643 (1961). [442 U.S. 735, 737]

I On March 5, 1976, in Baltimore, Md., Patricia McDonough was robbed. She gave the police a description of the robber and of a 1975 Monte Carlo automobile she had observed near the scene of the crime. Tr. 66-68. After the robbery, McDonough began receiving threatening and obscene phone calls from a man identifying himself as the robber. On one occasion, the caller asked that she step out on her front porch; she did so, and saw the 1975 Monte Carlo she had earlier described to police moving slowly past her home. Id., at 70. On March 16, police spotted a man who met McDonough's description driving a 1975 Monte Carlo in her neighborhood. Id., at 71-72. By tracing the license plate number, police learned that the car was registered in the name of petitioner, Michael Lee Smith. Id., at 72.

The next day, the telephone company, at police request, installed a pen register at its central offices to record the numbers dialed from the telephone at petitioner's home. Id., at 73, 75. The police did not get a warrant or court order before having the pen register installed. The register revealed that on March 17 a call was placed from petitioner's home to McDonough's phone. Id., at 74. On the basis of this and other evidence, the police obtained a warrant to search petitioner's residence. Id., at 75. The search revealed that a page in petitioner's phone book was turned down to the name and number of Patricia McDonough; the phone book was seized. Ibid. Petitioner was arrested, and a six-man lineup was held on March 19. McDonough identified petitioner as the man who had robbed her. Id., at 70-71.

If the police had installed 5 million pen registers on every resident in Maryland with the intention of leaving them in place forever instead of one pen register on the phone of a suspect of a criminal investigation I'm not convinced that even this conservative Supreme Court would have found that constitutional. I'm not a constitutional lawyer but it seems to me this is a slim thread to hold up the legality of the collection of all the phone call metadata of every American every day forever and saving it in a massive government server.

The ACLU is trying once again to bring a case to the Supreme Court and now, because of Snowden, they probably will be able to prove standing so we may get another decision. The ACLU must not believe this 1979 case settles the issue.

3. 10 NSA officials have permission to give information about US citizens to the FBI
There are 10 NSA officials—including Inglis and Alexander—involved in determining whether information collected about US citizens can be provided to the FBI. It can only be shared if there's independent evidence that the target has connections to a terrorist organization. Inglis said that if the information is found to be irrelevant, it must be destroyed. If the NSA mistakenly targets an American citizen, it must report this to the Foreign Intelligence Surveillance Court.

If this is true, then I would have no problem with this facet of the program.  There is always a balancing act between safety/security and individual privacy and liberties. The above example seems reasonable given the real threats out there. 

The link to the June 16, 2009 NYT piece that the Wired article gives no longer works, but I adjusted the url and found it, it's here:

http://www.nytimes.com/2009/06/17/us/17nsa.html

For those with access, it's really worth reading. First it's a "dejas vus allover again," or "everything old is new again."

Second, for someone interested in researching the facts about Congressional work on this in the past, and  trying to figure out if anything had been changed by the Obama administration or the Congressional committees at that time.  It is about both specific abuse incidents at the time or before and also about the same general program, and about the Congressional investigations into both at that time, especially those led by Rush Holt.

Article also says that In April, the Obama administration said it had taken comprehensive steps to bring the security agency into compliance with the law after a periodic review turned up problems with “overcollection” of domestic communications. The Justice Department also said it had installed new safeguards

The article doesn't really solve the disconnect between those two points, it's like just reporting the start of the hullaballo on these abuses (i.e., Rush Holt et. al. investigations, Obama changes a couple months before), There's a suggestion that Obama admin. may have fixed the problems that Congress were investigating, but that's not clear. But has got a lot of detail that suggests this is not all new news to the Congressional committees that deal with it. Suggests to me that the reactions now of people like Senator Feinstein, i.e., "we know about this, we worked on the flaws" were not disingenuous.

But one would have to follow up with subsequent articles/reporting to find out what happened, because this article is obviously reporting right in the midst.

So we should shrink the intelligence apparatus to a size so small that we can drown it in a bathtub? Should the US stick to just typical shoe leather investigation? If other nations use cyber-attacks, how should we respond? What is your view of the limits of electronic surveillance?