I think people are arguing over the theoretical, reasonable, practical, and benificial here. For me, all things considered, it was best to do a clean install.
1) It is a fact that there are system directories and files that apps, tools, and mucking around with oneself will alter performance -- boot performance and running performance. (I've personally seen VPN software, virtual machine software, Mac ports of Linux tools, specialty drivers, and other how-to- instructions modify system files and add things to special startup directories.)
2) It is a fact that I personally don't physically have the mental capacity needed nor Mac OS X expertise needed to remember all of the various tool installs and sudo mucking with system files that I've done over the years. It is also a fact that I don't have all the knowledge of all the changes all of these tools have themselves done to my system files. So without a clean install, I personally can't get a pristine system back - ever.
3) I have experienced, absolutely, that Mac OS upgrades are considerate of my previous application and tool installs and tweaks I have made to my system files and directories. I have witnessed upgrades leaving my system files and directories (including startup files and directories) that have been tweaked alone -- or careful not to delete anything added. And I have seen upgrades wipe out and rewrite those very same files if they were never altered.
4) It is a fact that with non-infinite resources, I could learn myself or hire someone to manually put my system back and all of it's startup files and directories back to pristine condition such that an upgrade or clean install will get me the same system performance. And sure, another options is I could clean install Lion and then subsequently upgrade to Mountain Lion. (But then I think we're back to the same argument for Lion.)
Fact: A clean install of Mountain Lion was the least effort for me to get the pristine system and pristine performance I wanted.
And as an interesting bonus. I had the experience of the default settings and apps for Mountain Lion. It was very interesting and I learned things I wouldn't have learned if I had done an upgrade. It was interesting to see some new features that I would have missed with an upgrade. For this reason alone, I'd probably do a clean install again on the next major release.
Erik