Ducatis have never been as quick as the fastest Jap bikes; this isn't a new phenomenon, nor particularly related to the 999.
But I'n sure there's a sizeable sector of the market who don't use that as their principal criterion for buying a bike. Like the members of this forum, maybe?
It's up to Ducati to attract this sector with bikes they want to buy. And it's not really about about subjective opinions about whether the 916 or the 999 is the better looking bike (although of course we all have opinions on that). There's more fundamental matters to consider.
For example, as even the champions of the earlier bikes must admit (and I guess I'm one), they had, to put it kindly, certain "issues" which may well have put people off buying them. This list includes (and is not restricted to: we can all make our own) short-lived clutches, dodgy rectifiers, high servicing costs, and discomfort for many riders. Whatever the 999 has succeeded in, it has largely failed to address these issues (except, partially, maybe, the last). Not only that, but it has introduced flaws that the older bikes didn't have, such as hydraulics that seem to require bleeding every five minutes, and non-user-friendly electrics. Build quality, far from improving, has arguably deteriorated. It's my firm belief that one of the main design factors for the 99 was "make it cheaper to assemble".
Ducati had some flawed, but still well-liked bikes. They have failed to build on that legacy, and fairing shape is the least of it.