Okay, so firstly forget around 80% of this thread on the 'he said, she said' is it for track, is it for road. Just forget it.
You've already made a very valid point on the cost of the 1299 + new system vs getting the R. Sounds like you've already convinced yourself?!
I have the Panigale R and bought this over the 1299, that was my personal choice. I chose it due to a number of reasons.
I was never really able to get on with the electronic suspension of the older R or the 1199 S. To have high end Ohlins mechanical suspension that I can set with a spanner is more up my street as I'm a bit old school, can't beat it.
The handling and the steering is sublime. This thing is so light it's itching to tip into corners with hardly any input. Breaking deep well into corners is awesome.
Also, when I got the 2014 R and compared it to the 1199 S, I couldn't help but feel a bit disappointed for the money I spent. The new Panigale R is incredible, the engine is just pure witchcraft, seriously, that is worth the extra alone.
I could also spend most of the day just looking at it, it really is a thing of beauty.
As for track/road riding a lot of the people here are forgetting is that both machines have 205 bhp and weigh nothing. Is that really suitable for the road anyway, where on the street will you ever fully use 205 bhp? Unless you're a d#ck! And both will be formidable weapons on the track.
Will the 1299 be a better bike for the daily commute, sure......... but will a well set up R?! There's no real answer here.
Get what you want, get what makes you smile the most. Both are great machines undoubtedly. But if you want something a little bit more unique, not a 1299 or an 1199 but a Panigale R, it really is a different experience.
............
The headlights are a bit sh#t though, high beam is decent enough, so if you are planning on night riding and really want the R, either upgrade them or choose a well lit route. It's not that bad, but they could be better.