I read that the second generation of this lens had some quality control issues and that it was a tossup whether you got a real sharp one or one of the less sharp ones. It is a problem that Canon is aware of. I suggest you tack up a target, some printed material with sharp edges, on a fence or wall where wind won't bother it, put your tripod mount on the lens, take it off IS, lock up your shutter, and use a remote trigger or the 10 second timer, in a bright but shady area, set the aperture on f7.1 or f8, the sweet spot for the lens, on AV, all to avoid camera shake and see what the results is. Turn off autofocus and focus manually. If you don't get tack sharp pictures, take it up with Canon. As I said, they know the problem exists but don't seem to be inclined to do anything about it of their own volition. I don't know if they would deal with it even if you bring it up to them but it's worth a try. They'll probably have you send it in. It can be two things not related to bad glass. One is that it may need to be calibrated, which will have to be done by them, and the other is that it may need to be checked for proper focus which you can do. The one you can do is referred to as auto focus micro adjustments and you can find out how to do that here:
http://www.northlight-images.co.uk/article_pages/cameras/1ds3_af_micoadjustment.html