Once you get used to the Nikon, you won't notice the reverse rotation of the focus and aperture controls. It does feel odd screwing the lenses onto the cameras in a reverse rotation though. It will be difficult if you have other cameras that focus the other way, every time I switch to my Pentax I have to deal w/ that.
Not all the AF lenses are created equally, including the Canons. I used to shoot an 80-200 2.8 ED lens on an F4 (my left shoulder is in bad shape due to this), and that bazooka was built like a tank and almost as heavy. But, it sure brought the shots in every time, and great bokeh on those. By and large, I've found the AF Nikon lenses to be very sharp, but only a few of their lenses have decently smooth bokeh.
As mentioned, all the AF lenses, of any manufacturer, will wear out and break much more often than the manual focus lenses due to their construction. Can you switch to MF lenses? You would have a lot more options that way, including the ability to put 3rd party, high end lenses like Leicas and Zeiss on your camera(s).