I know BMW had a final drive issue (reportedly affecting 5% of the BMW's) but I don't recall shaft drives being particularly bothersome on Japanese bikes...or Moto Guzzi's for that matter. I hate to think how many millions of miles have been put on Goldwing's and FJR's shaft drives since 1976, and although I am sure there have been some failures, I'm also sure that number has been so small as to be considered outliers.
Although today's chains are less problematic than they were prior to the invention of the sealed O ring and X ring chains, they are still problematic, in that if you ride a chain drive bike on a tour, you cannot take off without the tools and lube to service that chain on the road. Nobody I know takes off with tools to service their shaft systems. Additionally, many of us have driven a hundred thousand miles or more on shaft drive bikes with very little maintenance, some moly on the splines and a few ounces of rear end fluid once a year. If you ride 100,000 miles on a chain drive bike you are for certain, without doubt, going to have to change out the whole system, chain plus front and rear sprockets, at least twice probably more.
Didn't WOQNX just turn over 350,000 miles on his ST? Wonder if he has had a shaft failure? Can you imagine how many sets of chains and sprockets he would have had to replace in that mileage had his ST been chain drive?
Chain systems are very reliable (although they do fail too), relatively cheap to manufacture and replace, but IMO best used on motorcycles not meant to be ridden a lot of miles because of their finite life. At least that's my opinion. But like I said earlier MOST motorcyclists don't ride many miles and don't keep their bikes very long, so a chain for them is not an issue, they are never going to replace it anyway.