For me, it was mostly price. Both bikes are ugly to the point of looking good so neither bike won that battle, though I wish my ES was available in some actual color, instead of primer gray/black! Both motorcycles represented a substantial leap forward in performance, safety, comfort and technology from my KLR, so no issues there.
Initially, I tried to buy the GS because I had never owned a German bike and wanted to try one. Then price negotiations commenced. Two BMW dealers, only sorta close to me, quoted msrp and wouldn't budge. Both offered useless in-store discounts off retail for accessories and gear I already own. A local Yamaha dealer, 10 minutes from my front door, showed me he was interested in earning my business by giving me a price I could not ignore. I have no regrets.
I have never personally witnessed a BMW final drive failure. I have witnessed a bashed sump on a Tenere. Every bike has it's issues. Owning the Yamaha started about $6,000 cheaper and will probably continue to be much less expensive to own in the long term.