I doubt you'll ever find a conclusive argument as to which of the lens lines is "better," so I suggest you approach this from the perspective of what you want to see in a camera body.
I have a few dozen Canon FD lenses including some standouts like the 35mm f2 "chrome nose" and FDn 135mm f2, and FDn 24mm f2, and have always been happy with them. There are very few "dogs" among the FD primes, and as others have pointed out, they still tend to run a little cheaper than the Nikons.
However - I pretty much only use them on my Fuji X-E2 w/ Metabones Speedbooster, because I find most of the Canon FD film bodies to be problematic in one way or the other.
Canon made relatively few FD bodies with aperture-priority exposure. The most important are the A-1, New F1, and T90. The T90 is a lovely, versatile machine but working examples are getting scarce. The New F1 is a beautiful machine as well, and IMHO one of the greatest manual exposure 35mm SLRs of all time, but aperture-priority exposure requires an ugly AE prism that is also getting scarce and expensive. That leaves the A-1, which gets the job done but is plasticky, over-complicated, and often needs a minor repair to address "shutter squeak."
If you know that you are going to be shooting primarily the 50mm focal length and aperture-priority AE is important to you, consider taking a look a the Minota X-570 and MC Rokkor 50mm f1.4, which can be picked up cheaply and has a great feature set. The lens is very Leica-like in it's rendering.
If you are looking to shoot primarily shutter-priority or program AE and want to stick with Canon FD, consider the humble and homely T70, which is cheap, reliable, takes AA batteries, and has a huge, bright viewfinder - one of the best MF SLR finders I've seen.
I'll leave it to others re: Nikon as I've little personal experience there.