I actually think that making a choice between Canon and Nikon based on lens quality is a mistake. There are very serious photogaphers, whose living depends on their cameras, using each system. If there were grave across-the-board differences in lens quality, I doubt that that would be true. If you're making a choice between systems, and want to do serious research, you first have to figure out your own personal goals. (If your personal goal is, "I dunno, I just want to shoot everything," that's not very helpful.)
But IMHO:
A top-end Nikon has a better flash system, weighs less, and for a given effective field of view, uses shorter, faster, cheaper lenses, and has better sharpness edge to edge across the picture frame; and the body is cheaper. If I were doing wildlife photography, or a lot of hiking, or a lot of macro work (Nikon's close-up flashes are great), I'd go with Nikon.
I would say autofocus is pretty much of a toss-up.
A top-end Canon puts more pixels on target (though it may take a longer lens to do it), has better high-ISO by at least a couple of stops, better image stabilization, better tilt/shift lenses and possibly better ultimate picture quality for any given field of view. If I were doing lots of indoor low-light non-flash work (weddings), night shooting, or architecture, I'd go with Canon.
I personally think much of ergonomics has to do with what you become accustomed to -- but I've heard many Nikon people, who shifted to Canon, complain about Canon ergonomics; I haven't heard the reverse, though perhaps because most of the shifting has gone from Nikon to Canon.
By the way, Thom Hogan, who has a Nikon-oriented website, is predicting that the next Nikon top-end pro camera will be a ~23mp full-frame, to be announced in a year or so. If you go with a Nikon system, this might not be a good time to go overboard with DX-only lenses...