Sound is an important one for me and when you dish out the extra bit of coin to get an Akra system or something equally high end that opens it up, all of a sudden you have something that to most won't come off as a YamiFZ10 sounds better, smoother and is a better real world street bike. IMHOP.
i have been looking into the s1000r for quite sometime, until the fz-10 was announced state side. It seems like the closest naked version of a super sport to me. I seriously question the reliability of it though. If you cruise the s1000r forum, there is a disturbing amount of problems with premature wear on cam bearings, water pump failures, and some issues with stalls while downshifting that seem pretty common. So best to pay for that extended warranty on the bmw...
I have owned(not nicely either) 4 yamaha sport bikes over 16 years, and have 100% confidence in the yamaha brand.
An fz-10 will be cruising down the road while that refined bmw is in the shop.