Our staff of 12 photographers at the paper I work at switched to Canon last year after using Nikon since the 60's. There are several reasons but the biggest reason is that we were constantly getting cameras repaired for stupid reasons, ie., back focusing, rubber falling off the cameras. And Nikon's service started to stink. Even with our priority connections repairs were taking way too long. And the files just aren't as nice out of the camera as the Canons IMO.
So we spent in the neighborhood of $100 K making the switch. And I couldn't be happier. The Canon files are so much cleaner, especially at the high ISO's. Though Nikon is starting to catch back up with their newer cameras.
But let me clear up a couple misconceptions. First, with the Nikon lenses and motors. The older Nikon lenses, and lower line ones, are driven by a motor in the body. The newer, upper line lenses have the motor in the lens as do the upper line Canon lenses, making them focus just as fast. But I think my Canon lenses hold focus much better, with less searching then my Nikons. This is comparing both companies top line lenses.
Second, I don't think either one has a broad advantage in either upper line, or lower line. I think there are differences between comparable bodies and lenses though. For example, I'll take my Canon 16-35 over my old Nikon 17-35 any day. Same for my Canon 10-22 versus my old Nikon 12-24. The Canons are noticably sharper. But while my Canon 300/2.8 IS is as sharp as my Nikon 300/2.8 AF-S was, the tripod collar is the dumbest design I've ever seen. Though you probably won't take either underwater.
Comparing 70-200's, I'll take the Canon. I gave back my Nikon 70-200 VR and was using an older 80-200 AF-S because the 70-200 couldn't hold focus on anything. It was terrible. But the VR worked nicely.
I also like the smaller focus points of the Canon over the Nikon focus points. They work better on smaller objects IMO.
The strobe systems are a wash for me. Neither TTL system is as good as they were with film cameras. I do really like the Canon wireless TTL though. It works pretty well
The issue with lens compatability is not a big issue IMO. Canon took their lumps in the
80's when they went to their AF system making it imcompatable with their old cameras. Nikon retained customers but at the expense of a faster AF system. Nikon finally started to catch up in the late 90's but by then it was too late for many. Sure you can use some old lenses on your AF Nikon but you can't take advantage of any of the good features such as TTL. At least not without getting the lens converted.
Canon has lenses that will only work on their smaller sensors such as the 10-22. Nikon has DX lenses that only work on their Digital cameras. I like the 1.3x crop factor of my Canon EOS 1D MKIIn's over the 1.5 crop factor of the Nikons. My 16-35 is still a workable wide angle lens. With my Nikons I always had to carry a 14mm to get a good wide lens. PITA! I do shoot a 20d UW though, with a 1.6x sensor, so I have a 10-22 for it.
It's funny that UW you see more Nikon shooters but in the world I work in, photojournalism, you just don't see Nikon as much anymore. They are still there but Canon is completely dominating. Wonder why?