I paid about $17,500 for my K1200RS in 1999.
It now has about 72,000 miles with only one repair (recent rear main seal leak).
I figure if I ride it another 5 years and then drive it into a canal or just give it away, it has cost me $1,750/yr for basic ownership/depreciation (exclusive of gas/tires/routine maint - which you'd have on any bike).
Hopefully I'll get SOMETHING for it down the road, so that should result in even less overall cost.
Yamaha makes fine bikes, and I've owned a few (below). The Yamaha would make a great sport-tourer - assuming the heat issue has been addressed.
OTOH, Yamahas seem to wear a bit more cosmetically, esp. if left out in the elements. Rusting fasteners, eroded clearcoat, etc. BMWs generally wear very well in this regard.
In short, if you plan on keeping a bike for the long haul, it can be worthwhile to spend a little more. If you turn them over every few years, probably not.