I have had 2 E60 M5's now and i have only had 1 problem between the 2 of them and that was the Vanos oil line leak. The problem was fixed in less than a day in the shop and I was given a nice M5 model for my trouble. My E39 '02 M5 spent a total of 1.5 weeks in the shop the 7 months I owned that car.
There seem to be a few problems and not common to every car. However, they do fix the car under warranty and IMO the E60 is far superior to the E39.
I don't know any actual numbers for used E60's, however, maybe one of the reasons is the lack of great gas mileage??? Maybe they were talked into buying the cars at the dealer and had no clue what they were really getting?? Got the old, "you need to have one of these", "very exclusive car", "we have a year waiting list, but we can get you this one now!". just some thoughts.
Good luck!! They are wonderful machines!! I would give the SMG a chance, you won't regret it!
Robert