I came off a Panigale 959. Loved it for what it was but needed something for the occasional Two-up. Marital harmony and stuff like that.
My Monster 1200R is now my Hooligan / Sport / Track bike. Wife didn't like the Monster. Too loud and rambunctious.
My dealer was very accommodating and a great salesman. I was lent a Multistrada 1200S for a total of at least 1000Km in aggregate. I had to buy one.
I bought the 1260 Pikes Peak. No regrets.
The only thing I thought I would possibly miss on the Skyhook was the Urban mode for rough patches of road. That's it. Otherwise, it's always in sport.
I wanted the light Forged Marchesini's and the Ohlins.
Ohlins are easily serviceable. Everyone has parts and knowledge for these. Skyhook not as much.
About the ride: Ohlins are sublime. Now that I've had it, I don't miss the on-the-fly adjustability. Suspension is a dream.
How often have you changed the settings on your Panigale 1299S? That should answer your dilemma.
A friend of mine..a wise man.. always says; " Go big or go home".
PS. Irrelevant of your choice, You're going to change the stupid OEM tires. I'm already at the edge and I haven't even dragged anything....and I have a center stand! While I'm not suggesting Supercorsa's, Diablo Rosso III at a minimum based on back-road scratching.