Alistair - interesting points, not many of which I'm knowledgeable enough to answer!
As I understand it, the point of the standard was to try and codify how innovative companies went about being innovative, whatever their profile (in the sense of what they did and how they looked to the outside world). As far as I know - though I'm quite willing to be corrected on this! - the UK was the first to attempt this. So to this extent we were ahead of the curve.
Obviously, as you say, not every element of innovation can be codified. In fact, some would argue that it's almost a contradiction in terms - and there'll always be a need for that magic ingredient you mention. But the theory was that if you could codify the process of the thought leaders, if only to some extent, it might help other firms become more innovative too (not by using it as a how-to manual, but as best practice-type tips).
So the standard was never going to make non-innovative companies become innovative - but the idea was that it might help those with an interest in the area to structure and manage their innovation so it would lead to concrete results. This seems quite sensible to me, which is why I think it's a wasted opportunity..