perception is reality. I've no doubt there are cases that upgrade in place doesnt work as well as fresh install, but I am skeptical that there is dramatic demonstrable differences between the two most of the time.
I believe it's likely more a benefit of clearing out the cruft that has accumulated over time rather than problems with the update itself. A lot of stuff gets installed over the years, and upgrading in place keeps the majority of that in place. Doing a fresh install and putting back only what you're currently using will probably result in fewer programs, daemons, drivers, etc that the system has to deal with.
For yosemite, I have a macbook pro that came with the OS and another macbook pro (nearly identical) upgraded from mavericks. No significant differences. I don't see why it should be like that this time and I would love to read a technical explanation.