There is "only" about a 3k difference. And that is close enough that if somebody was already going to spend $16k, they could think "we'll ...., I might as well get a Ducati". Which is exactly why you are seeing them flooding the market.
You used to could get a new Liter bike for $10k. Those days are gone. But with that being said, there used to be a pretty good performance and technology difference between Ducati Superbikes and Jap Superbikes, and those days are gone also. Somebody can lap the track just as fast, if not faster, on a base R1 or ZX10 as they can on a Panigale R.
You can still get Japanese liter bikes for around 11-12k. Black Friday sales have 2015 gsxr750 listed at only 9k and 8k for 600s. Even still, I'd get an RSV4 over any one of the Japanese bikes.
The R1M is the comparo to the 1299S not the R model. So $21,990 R1M vs $24,995 1299S. But the R1M is still cheaper by $3K from the S Model. For what you get it's a hell of a deal.
I am also under the impression the R1 will go up in price about $500 also for 2016.
It looks like 2016 and 2017 are also going to be good years for sportbikes with Suzuki and Honda coming back to play.
You can still get Japanese liter bikes for around 11-12k. Black Friday sales have 2015 gsxr750 listed at only 9k and 8k for 600s. Even still, I'd get an RSV4 over any one of the Japanese bikes.