The experiences I've had with Canon are that the glass has gotten better, the build quality went down but has since gone back up.
Example: going from FD to EF was in the 80s, when plastic was fantastic. My FL 55/1.2 is a great metal beast, optically great except some wide-open coma (gone by f/2). My EF 50/1.8 II is a toy. They even used to make the EF 50/1.8 (mk1) with a metal mount, then changed it to plastic to save a few bucks. Optically, I can't compare it to the FL55/1.2, but from what I've seen it's not that much different to the FD 50/1.8. They've had problems introducing lenses with new optical formulae, eg their first versions of their digital lenses were shocking, and their cameras got a bad rap because their kit lenses were so bad, ie 18-55mk1. But lately they've gotten a lot better, even for the price, my 40/2.8 pancake is great, you can get them for $150 nowadays, and mine spends its life glued to my EOS3 with an orange filter on the front, damn fine lens.
When Mamiya 645 transitioned to AF they also kept the same glass, just re-mounted them in an autofocus barrel and added an electronic diaphragm. I recently tried getting a 45AF to replace my 45MF. Glass was good, but the diaphragm was DOA, wouldn't stop down or open up, which is kinda useless, so I had to return it. Build quality looked a bit more plasticy compared to the MF tank, which probably contributed to it breaking easier, but the glass was the same. (They've recently re-formulated a lot of their lenses to make them work better with digital, but that's not directly related to being AF).
I have heard things about Nikons, especially the 20mm primes (that I was looking at getting once), in that the first ones were a lot different to the second ones, some were sharper in the centre as a trade-off for more distortion or softer corners, can't remember which was which though...
