There isn't any "R" model - in Ducati's entire Ducati's superbike lineage that is more expensive to maintain than SP, SPS, S or standard models.I would get the 1299S if it were me. While the R models are very sexy I've heard they are considerably more expensive to maintain. The upgraded electronics on the 1299 is what I'd be after. Of course I would use it as a track bike though. With that said go for the new Monster 1200R. But again more expensive to maintain
Unless you're replacing internals. Only then does it become more expensive. E.g.: titanium conrods, valves, etc. And there are exceptions - like some of the SPs and SPS which have those more expensive internals.
That said, I'd go with the 1299. It's a 100 more ccs. And not as expensive as the R.
Unless you get a used R. Then you'll become a member of club "Exclusive".