I picked up a 2016 Panigale 1299 S a few weeks ago and finally had a chance to ride it on Sunday (I work 6 days a week and weather hasn't been all that great lately), and put about 40 miles on it.
Today I am sitting here contemplating on selling the stupid bike. And here is the reason why. While riding on the street like a normal human being, the bike simply doesn't work. Every turn I make on the street is a gamble with my life on this thing. Its nearly impossible to modulate the god damn throttle to make the POS turn smoothly without it bucking or surging, even in WET MODE with all the electronic aids turned on! What is the point of riding a bike that has such a huge learning curve and high risk factor? Sure, if you're a dare devil or an adrenaline junky, the story might be different. But I am not willing to take that kind of risk with my life. And having paid close to thirty thousand dollars for this ....... garbage, using it only for track seems like a huge waste, because I paid a hefty premium for those ridiculously unusable headlights, turn signals and mirrors. In every aspect, this bike is nothing more than a showoff piece.
Some people say this bike is an "angry machine". Well, currently I am angrier than it, because I bought into the hype. Last time I rode a Ducati was when they came out with 1198 with a big hype surrounding it just like they do with all of their new bikes. When I test rode it, I absolutely hated it. I just don't understand their logic and their concept of making gazillion ft.lbs of torque at low rpm range which cannot be predictably controlled. Ducati chose the wrong path with their engine concept. To me, it was a ...... up design from the start and they were stuck with it. So they had to patch it up as much as they possible could, wrap it up in pretty plastic covers and had their marketing team go to work.
And so many years later, they still carry on their stupid concept. It doesn't matter riders couldn't handle 60ft.lb of torque 5 years ago, ducati is going to make a 100ft.lb torque machine where riders only used 5% of its power on the pavement they ride 90% of the time. And they didn't care that the 80% of its power could not be properly managed on the street, because its a "race bike", "you have to be angry to ride it" (are you ....... promoting road rage?), "just ride it faster" (and kill yourself)?, get an aftermarket ECU modulator (which may not work) and pay another grand on top of what you already paid for the "most advanced bike in the world?" c'mon! Give me a break!
Ducatis arrogance is appalling. Their attitude is simply irresponsible and it clearly shows that Ducati as a company does not care about the safety of its consumers, but rather consider their customers to be a bunch of ....... with a death wish who will eventually Darwin themselves out using the crude tools they've provided.
I foresee that Ducati will dump their engine design in the near future, because as I have mentioned, they were stuck with a ...... up design by hiring a monkey for their engineer, and soon move on to a completely different design or follow suit with other manufactures and admit their flaws.
I had a 2011 BMW S1000rr and by comparison, its a far better bike than the Panigale.
Nanoplastic I feel your pain! 
I had the very SAME issue with my bike.
I want to state this right up front.. It has NOTHING to do with the way you ride... Others on this forum that are telling you that "it is you not the bike" obviously didn't have the same problems as your bike has or my bike had...Others on the forum told me to "just live with it" or that that is just the way the Ducati's are and that was part of their "Character"
.. Well I called ........! Mine did the same damned thing and worse.
Mine also would have the delightful problem of the throttle sticking at around 3000 rpm when coming to a stop light (then suddenly drop off).. That is very dangerous in a corner..
Like you, I had to keep it above 5000 rpm or it would buck and act like it was going to stall... I went through a lot of crap and countless times in the shop while the dealer tried adjusting the throttle body syncs and even reprogrammed the ECU with a Nexxer unit. All to no avail... I even purchased the new Akropovic exhaust with the so called Racing "UPMAP" no big change... That cost another $3600.00
Finally I fixed the surging problem by installing a RapidBike racing module which auto tunes the bike as you ride.. The problem is that Ducati had to lean these bikes out so much to pass emissions and noise tests that they are very stiffled.. If you try to use most fuel modules the bikes factory ECU will auto correct itself if you try to use a Power Commander or Bazzaz unit. The Ducati factory has made these bikes a very proprietary machine that will only accept certain modifications....I guess they dont like others to get into the act.. Hell I could not even find an aftermarket windshield that will fit the 1299... It is different than the 1199..
Well I finally got mine working right and it has nothing to do with the modifications from the Ducati dealer etc..
The ONLY modification I found that works for the surging issue on my bike is the Rapidbike Racing Module. It comes with a good base map and ignition map. You hook it up and ride it.. then it starts reprogramming itself as you ride.. It REALLY works well and is the best value for your dollar with this machine.
It actually will adjust the low to mid throttle throttle mapping if you hook it up to the stock low band O2 sensors.. The others like Power Commander and Bazzaz do not adjust these off throttle areas much.. They primarily adjust the mid to higher throttle settings only ** I also installed the Sprint filter which flows much better.. My bike is a TOTALLY different machine now and runs the way it should have from the factory.. It is a shame that a guy spends that much money and has to spend another $900 to $1000 just to get the bike to run right . It is atrocious how they de tune these bikes to meet the EPA etc. regulations from the factory..
Now all I have to contend with is the problem of the bike dying on me at intersections or parking lots or in the middle of traffic etc. every once in a while out of the blue with NO warning....Evidently, that is a problem that the 1199 and 1299's also have.. If it hasn't happened to you then you are lucky..
BTW.. The dealer finally figured out why it was having the throttle stick on de acceleration in first gear.. After they had replaced the ECU the complete throttle bodies etc. The mechanic tried re programming the ABS and traction control programs and THAT fixed it.. It only took 5 months to finally get it right..
Now all I have to do is figure out why it suddenly dies on me in the middle of traffic about three times a week..! Oh well after all it IS a Ducati right? I guess we are just supposed to put up with its "idiosyncrasy's" Kinda like dating a beautiful Italian Supermodel Beautiful but you have to put up with a lot of expense and other .... to keep her.. LOL
Good Luck I love my bike (when it is running well) but to tell the truth, If I had ANY INKLING of what I would be going through I would never had bought it either.. The Japanese bikes are so much more reliable and trouble free.
Those Italian's could learn a thing or two from them..
Speedy
