They were bothered that their "stingray" like devices could not capture the messages. But fear not, they can still get it from Prism or Xkeyscore (or whatever they call it).
The article linked complaints that traditional legal interception means do not work. Those are the ones where they nicely ask the cellular providers for the data. It's not about "stingray like devices", it's about sending a letter and getting the data. End-to-end encryption protects against that, be it iMessage or BBM.
Prism collects data directly from companies that participate, and Apple has said they do not have access to iMessages contents. There was some speculation about courts being able to force Apple to abuse their authority as the iMessage certificate swapper, but I've seen no evidence or convincing argument for that to be the case.
Xkeyscore does not collect any data, but searches it.
Is that seriously what you believe?
You cannot perform an audit on your own. You are trusting that you received the correct keys without a way to verify identities outside of the network.
That is not secure. Please read http://blog.quarkslab.com/imessage-privacy.html
White paper on the topic: http://blog.quarkslab.com/imessage-privacy.html Consumer grade article: http://arstechnica.com/security/2013/10/contrary-to-public-c...
Lavabit offered in-network public key encryption for its users. Its implementation was faulty and investigators only needed an SSL key to get the information they wanted from suspects. They also ordered Lavabit to keep operating under the pretense that they were secure. http://www.infoworld.com/article/2609583/encryption/how-secu...
Skype was advertised as "end-to-end" encrypted AND peer-to-peer networked for years, until it was slowly exposed as a lie. Skype's content is not end-to-end encrypted and the network is centralized. http://arstechnica.com/security/2013/05/think-your-skype-mes...