As a pro wildlife photographer with 10 years experience of Canon cameras (40D, 50D, 7D, 6D, 5DMkiii, 7DMkii with L lenses), I can assure the doubters that there are definitely some AF issues with the 7DMkii.
My body, (8000 shots since purchased in January), works fine in some situations but terribly in others, despite lots of experimenting with multiple variations of AF settings. My 5DMkiii, on the other hand, which uses exactly the same system of "cases" does NOT suffer from any these issues.
The first issue:
My 7DMkii focuses extremely rapidly when set to one-shot or AI focus, with any focus "case", and any focus area selection. However while the end result is razor sharp, the image in the viewfinder is slightly out of focus, which is rather disconcerting. When manually focusing via live view, the live view focus and sensor focus are obviously in sync. The problem cannot be compensated for by AFMA - it lies with a slight misalignment between the viewfinder focus screen and the sensor plane.
Some other 7DMkii bodies apparently don't have this issue, so it is unlikely to be a design fault, more likely an assembly and quality control issue.
The second issue:
When set to SERVO focus (and focus priority for first and subsequent frames) my camera is slightly less reliable when shooting single shots, and absolutely useless when attempting to shoot in continuous mode. Even at 3 fps silent continuous drive, it can't keep up with even a large slowly moving subject! Setting the camera back to AI FOCUS immediately improves the hit rate, but is still nowhere as good as the 5DMkiii, and is more on par with the 6D.
The third issue:
My camera, when set to 65pt wide area focus, and set to AI FOCUS or ONE SHOT mode, always focuses on the closest object, regardless of its position in the frame. However with the same 65pt wide area focus, and no other changes, apart from setting SERVO focus, it acts totally differently, always focusing on an object in the centre of the frame, regardless of whether there is a closer object to the left or right.
Issues 2 and 3 seem to indicate a firmware problem.