My very unscientific opinion:
- in the pro lens arena, both companies are exceptional. One has an advantage over the other here and there, but overall the pro lenses from both marks are extremely good.
- Nikon tends to be better in the lower echelon of gear. While there is the odd Nikkor that isn't great, most low-end Nikkors (and particularly since the autofocus era) are extremely good. A good case in point is the exceptional AF 35-80/4-5.6D (first version), which was a dirt-cheap lens that has exceptional optics. I own one unapologetically. The results really are as good as my pro lenses can manage, if the slower maximum aperture isn't an issue. The Canon consumer-grade lenses tend not to be as good. They aren't awful, but they aren't as good in general.
- the bodies are a very subjective call. I prefer the handling of the Nikons (higher eyepoint, useful for eyeglass wearers, is one reason, but I like the control layout of most of the cameras). The Canons have a different style to them. Some prefer them, some like me don't. It's not better or worse, just different. There are some quirks in the pattern (the Nikon F70 comes to mind, which again some love but most hate).
- the backward lens compatibility is a double-edged sword. Canon's is much simpler. Autofocus lenses work on all bodies. There is no loss of capability, as long as the body can support the feature. In other words, any modern Canon EF lens will mount on an old Canon body and can do everything you'd expect it could do. (I don't think image stabilization is backwards compatible - I might be wrong on that point - but you get full AF.) Nikon's compatibility is far more complex. In some ways it's worse (the AF-G lenses are of limited utility on older autofocus bodies and essentially useless on older manual-focus bodies) and in some ways it's much better (many modern Nikon bodies work very well with manual-focus lenses, which lets you use classic lenses like the 105/2.5 or save money by making your 16/2.8 fisheye an AI-S instead of an AF-D). For me, Nikon's flexibility is better (and I've chosen bodies that work well with all of the lenses I have, which range from AI-converted 1970s lenses to a couple of modern AF-S lenses), but there is a much steeper learning curve.
- the pro Nikon bodies are generally more flexible than the pro Canon bodies. With the exception of the F6, the Nikons have interchangeable viewfinders. Many won't take advantage of this but some will. Even being able to remove your finder alone is useful, if you have to shoot, e.g., over the heads of people - turn your camera upside down, prism off, and shoot with your arms fully extended over your head. You can see - not well, but better than you can with a viewfinder.
Nikon fell behind for awhile early in the AF race. The F4 is an incredible body but it is not a great autofocus body. The EOS cameras of the day eclipsed it rapidly. It took Nikon several years to catch up. Nowadays the race is neck-and-neck in most regards so it is a question of what lenses and bodies you want to use.
Ultimately both are blown away by a simple Bronica or Hasselblad, so...

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