Great value on the last few leftovers, I had an S for a while as I got a bargain price in a used one when KTM were giving away new ones about 18 months ago, it was a really good all round bike.
My understanding is the 1090R is very well rated as an off-road bike with a better suspension setup than the 1190R - but I am sure the 790R is way superior so depends what you want, if i wanted to do off-road I would fine the little bit extra for a 790R, if I wanted to do predominantly road miles then the 1090R would be my choice...
...But as I don't go off road and mainly do European trips the 1290S is perfect for me,and there is no way I would take a £15k off-road, I have a 15 year old DRZ400S for such tasks - I can afford to drop that.