I own an 1199r and a full option s1000rr and installed Akra and power commander after a few months of ownership.
Question, do you guys think designer/engineers from both companies would design "Hey let us go make a slow , ugly and a bad handling bike. what do you guys think? let us make sure it will take 20 seconds to reach the rev limiter, use cast iron every where to make it tip the scales at 600lbs dry, let us make sure that the swing arm is crooked as with the frame, any thing that will hold the engine and forks will do. Let us make it look ugly so that the owners will cringe every time they sit on it and do not forget, make it so unreliable so the dealers will make killing with the repair". Definitely no superbike company will build a bike thi sway. For sure Ducati, Bmw and the other companies will design a bike that is fast, reliable and to their own accord, what they percieve as beautiful.
So it is no surprise that when you test the bikes out, the engines roar may it be a vtwin or an inline 4. it handles great and if your bike is built right, no bike will leave you stranded in a middle of nowhere. Manufactureres may experience a few bad batches here and there, base on this forum, the conrod failure of bmw's is a result of a wrong torque specs of a robot? correct me if I am wrong. As with the Pani, you can read on the forums about the complaints of other owners.
BMW is a good bike and it does not cook my buttocks the way the Pani does but the bmw is harder to turn but when you commit to a turn, it inspires confidence, at least for me. The Panigale is very light and very flickable, the power is up to par with the s1000rr but the heat it generates(at slow speeds) is close to unbearable.
For me, the bottom line is both are good bikes and both have quirks. Since this is a Panigale forum, ofcourse majority of us will vote for the Panigale R but we can not deny that the s1000rr has some good parts too, BMW engineers made sure that it will not be a bad bike. at the end of the day, it will be your call.