I have shot Nikon since the 1970's and just last week got a 1DsMk2. I'll be selling off all my Niknon stuff soon.
Accessing the menus is definately more of a pain because you have to HOLD DOWN one button with your left hand while you turn the selector wheel with the right. Fortunately I rarely mess with menu options... I set them and forget them. However you have to do the same hold-down-while-turning to review images in history, and that takes some getting used to.
Changing some settings (like ISO) require pressing 2 buttons at the same time with the left hand while turning the control knob with the right. If you shoot manual alot like I do, it is easy to accidentaly change the apeture unless you turn off the main control wheel.
Their raw conversion software is not nearly as good as Nikon's.
Canon's LCD is better and truer. Dynamic range and noise are better. Shutter lag is much better than my D1X. Battery life is very good.... much better than D1X, and more like the D100/D70.
I rarely use AF aso it is taking some getting used to to focus by rotating the other way.
The Canon AF is actually more useful/usable IMHO than Nikon's. I've used single point with automatic expansion, in one-shot mode while using manual AF activation with the button under the thumb rather an the shutter button.
The Canon 200mm 1.8 is a great lens... on par with my Nikkor 200 f2. I was asked to shoot some stuff at a concert Wednesday, and this is a full-frame shot at 320th sec at f2.0 ISO 1600 with the Canon.
Here is the same image at 1:1 pixels... no retouching, no post processing, no sharpening... just converted from RAW to JPG.
I shot RAW so if changing light levels caused under exposure, I could recover... on images that were clearly 1.5 to 2 stops under exposed from the ISO 1600 setting on the camera, they recovered nicely with noise levels vastly superior to the Nikon.