My first (06/2005) R12GS was a true nightmare. In 60000km/40000mls : multiple headlight bulbs, gear sensor, speed sensor, indicator switch left, indicator switch right, brake pump module, ring antenna, battery, corrosion, warped disks, all in all 3 break downs. Finally, when the servo assist went, I got fed up.
I was looking around for alternatives (Triumph, KTM) but when dealer gave me the best deal, I traded it in for a 12/2007 R12GS, hoping the teething problems would have been sorted out. I haven't regretted this swap, though the first 3 months' harvest was rear axle, warped disks (finally solutioned), and brake pump module (= 1 break down). Since then troublefree. Phew. I'm now at 36000km/24000miles.
Some problems, though not frequent in occurance, seem typical for the whole R12 range (FD, and right hand cylinder exhaust valve break down).
Then, BMW don't hurry to remedy well known problems (ring antenna and brake pump module took forever).
Furthermore quality levels go up and down as suppliers are switched frequently. The rear axle problem is typical only for 2007 models, for example. My 2005 model had WP suspension which wasn't too bad, but my 2007 was delivered with poor Showa's. And so on.
I'm sure the BMW quality issues frighten new customers, and lower resale values will make first time buyers think twice. And that's a shame, the bike doesn't deserve a bad reputation. It's a great ride, smile's on my face all the time (I know that's hard to believe). I love it, and haven't got a clue what bike to buy next.