Great detective work guys! Like Tomei, when I did eventually upgraded to iOS 6, it was with hope that it would cure my WiFi sync issues. It did not.
I limped along through several minor iOS update versions hoping the problem would be corrected. Nothing. After holding out for a few months, I gave in and upgraded iTunes from the suspect 10.7 version to the brand new, overhauled 11.x version. Again, the hope was that the new software would cure the syncing issues. It did not.
So at least in my case, the sync issues started not when I upgraded to iOS 6, but when I updated my iTunes to the first version that supported iOS 6.
This would be an interesting control:
1) Get hold of an iPhone running iOS 5 and try to sync with iTunes 10.6.1. Does it sync reliably over a period of several days?
2) If it does, upgrade iTunes to the latest version. Again, monitor syncing over several days. Still reliable?
3) If that works, upgrade the iPhone to iOS 6. Montior syncing over several days.
Depending on where syncing breaks down, that's your culprit. Any volunteers?