I have a 959. My buddy bought a 1299S. Both 2016's. We've ridden together several times. I included a couple pictures of our bikes together and a picture of my bike recently (with more mods done). Of course they look pretty similar.
My personal perspective is that the 959 is more rideable (for the street). And I've heard that underseat heat would be more of an issue for the 1299. The 1299 does have more power. But for me the 959 has plenty of power. I tried to talk my buddy into buying a 959 because of the big difference in cost. If I was going to spend the extra $$ for the 1299, I probably would go with the S version. But that's just my perspective. And I think the 959 is an amazing value.
That's just my perspective. Feel free to reach out if you want to ask anything more. Since my buddy has a 1299S, I'm in a position to compare both.