Why are people so upset that the Pope is reaffirming the stance that non-Catholic Christian groups are "defective"? If he didn't think so, would it make sense for him to be Catholic, let alone Pope? You know the old joke...
Look at it another way: Protestants (like me) presumably hold that the Catholic church is "defective" in its own way. Muslims think Christianity is defective. Atheists think it's all defective... We might as well be honest about it (without being unnecessarily abrasive).
I desire Christian unity, but I don't think ignoring over such differences is helpful. I would rather have fellowship with Catholics who take our differences seriously than those who would gloss over them for the sake of ecumenism.
On another note, here's a quite interesting attack by Scott Atran on the anti-religion program proposed (or rather, re-proposed) by Sam Harris, Richard Dawkins and many others. Naturally I would disagree with Atran (an atheist) on lots of things, but it's interesting to see him argue that the proposed program abandons reason, evidence and science.