With higher ISO there is some loss of micro detail which can appear to be softening, but is just the nature of the beast. Noise reduction also robs some fine detail. I notice that all your "BAD FOCUS" shots are higher ISOs.
BAD FOCUS 1 appears possibly to be camrea shake. It also could be that Image Stabilization was working but hadn't fully stabilized the image yet, at the very moment of exposure. That does happen and there can be a small number of shots ruined by IS, especially if you "shoot too fast" with it. Is this your first IS lens? Also, this could be subject movement. IS cannot help with subject movement. 1/80 is bordering on "risky", when shooting people.
BAD FOCUS 2 is an extremely difficult to focus subject. Actually the results look pretty darned good to me. The leaves on the left appear to be on the same plane as the tree on which you focused, so I'd expect them to be in focus too. In the sample image, the tree on which you focused appears pretty correctly focused.
BAD FOCUS 3 and 4 are dead on, focused right where you put the point of focus. I don't see any problem wiht them.
Do you ever shoot other than f2.8? Practically any lens will improve closed down one or two stops, even the 70-200 II, which is a great lens wide open.
Underexposure, then amping the image up in post production also adds noise and loses fine detail, adding to appearance of softness.
Different images need different sharpening during post-processing... depending upon subject matter, ISO used, size and type of final use, and more.
I would spend more time with the lens, work with it and see if it doesn't improve.
Also try making some prints on smooth, matte paper. That will tell you a lot more than your computer monitor. It can be a very big difference, in fact. Sometimes the resolution of an image just doesn't seem to match up well with the resolution of a computer monitor, I think. I'm using a calibrated, graphics quality monitor to view your images.
I don't hesitate to use my 5DII at ISO 6400 and find it excellent from 3200 and lower. But, of course, a lot of that's down to personal preferences.... what's acceptible, usable to me might not be to you, and vice versa.
Finally, do you have a filter on the lens? If so, you might try without it. Some small degree of softness or focus error can be caused by a filter... even a good one. Different lenses respond differently to filters. I don't use the 70-200 Mark II so can't say about that particular lens... but the EF 100-400mm, for example, really doesn't like filters. Telephotos usually are more forgiving than wide lenses, but you never can tell. Also, do you use the lens hood? Oblique light striking the front of a lens sometimes seems to cause focus errors or image softness. And, when using a filter it's even more important to also use a lens hood, to keep oblique light off the filter as best possible.
