FWIW (I didn't realize this either until the end), the article is actually pointing out that flame isn't lame for one very specific reason: the cutting edge cryptography research that went into it.

No. The article is pointing out that Flame isn't lame in lots of different ways, and saying that the naysayers kept calling it lame until one single spectacular bit of non-lameness came to light. It's suggesting that they should have cottoned on sooner. At least, that's my reading of it.

It's using lame as a response to this article: http://xato.net/malware/flame-is-kind-of-lame/

Apparently "gay" & "retarded" are horribly offensive & insensitive descriptors, but "lame" is ok. Who knew?

I suggest it's because it's not commonly used today for its actual definition.

People don't normally refer to themselves or people they love as "lame." Not so for "gay" or "retarded."

A modern equivalent of "lame" might be "handicapped," even though it is not as specific.