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.