This whole thing really pisses me off!
The most significant change I see is the bump in compression ratio on the R and reduction in weight. It will make the R a beast throughout the rev range. I don't know why they didn't bump the compression ratios on the 1299. With 87cc more they could of squeezed more than 10HP out of the engine. Ducati should of bumped the compression ratio to 13:2:1, Lighten the Con Rods, crank shaft, flywheel, change and lighten the internal transmission gearing and final drive ratios to prevent loss of HP in the drive train and more to the rear wheel and made the 1299 the flagship superior bike. But I guess because of the WSBK rules and its restrictions the 1199 R has to be the flagship bike so that Ducati is limiting the 1299 performance. The 1199 R will run circles around the 1299 due to its higher compression and loss of HP to the rear wheel. The "1299" is nothing more than a marketing gimmick to get consumers to buy with little gains.
The best value for performance wise I think is a toss up between the Base 1299 and R version. It will be costly to get the 1299 weight down to around the R's weight and to bump the compression up to 13:2:1 like the R. but you probably can do it close to the delta price between the base and the R (maybe a little bit more) but you will have a hell of a bike most likely out performing the R. I'm sure it wont be too long before they someone comes out with High Compression pistons/kits for the 1299.