I don't know where this myth came from that a clean install is better than an in place upgrade but it is simply not true. The in place upgrade works smoothly and there is little chance of any software incompatibilities. Any potential problems are identified with the Upgrade Adviser. The ONLY in place upgrade that is possible is from Vista to Windows 7 and it works (as far as I can tell) flawlessly.
If anything, the clean install is likely to present more problems when it comes to finding, installing, and configuring all the applications one might have then installing all the updates to them, and reintegrating all the output from them. And all that assumes there will be no problems with registrations when the applications are reinstalled.
If one is eligible for an in place upgrade, I suggest that is the best path and there would have to be some very good and known reason for electing to do a clean install.