"A recent Bloomberg piece points to a 2012 report on terrorism which found that most serious terrorists steer clear of the most obvious platforms—major cell networks, Google, Skype, Facebook, etc."
The 2012 report cited wasn't some senate oversight committee, a DIRNSA (director NSA) report, or a truly credible intelligence source. It was from the Dutch Intelligence agency, an agency focused on leftist activity vs. right-wing Islamic terrorism.
"In 2010, Google estimated that it had indexed just 0.004% of the internet—meaning the vast majority of the web is open for surreptitious message-sending business. Terrorists simply aren't dumb enough to discuss their secret plans over Skype or to email each other confidential information on Gmail."
Do you think that it's feasible for terrorists to use couriers/tradecraft to transmit all messages to their group members around the world? If I told you right now to get a message to your cousin in Connecticut within an hour without using Skype/email/phone or anything of the other means listed, could you do it? Let's say you answer that you'll just use steganography (http://en.wikipedia.org/wiki/Steganography) to hide the message. How are you going to communicate to your cousin where to look for the message and how to break it down?
Armchair intelligence analysis is the same as armchair anything -- you have no basis for what you're talking about except a bunch of redacted reports, news articles, and spy movies. Intelligence analysis is a very straightforward thing, though, which a lot of folks working in tech would be really good at, but articles like this are the equivalent of commenting on the merits of using PHP having never written a line of code in your life.
I understand peoples' frustration with what (if true) would be an egregious slight on the public trust. But, is it more likely that the 4+ million security clearance holders are in on some large conspiracy to take away our freedoms, or that a disgruntled worker wanted to watch the world burn a little. Having worked in every facet of the NSA as a linguist/intelligence analyst/programmer/many other things, and CIA contractor for a year, I tend to think the latter, and I'm very vocal about my thoughts on the intelligence community.
Read my previous comments if you want to see my thoughts on how the media has been getting it wrong, and what the deal is from the perspective of someone who worked in this community.