Apple is changing their privacy settings for iOS6 and deprecating device UUIDs (UDIDs). According to a WWDC presentation and the docs there are two replacements for the UDI
I suspect that Apple will simply reject your app if you use identifierForAdvertising for anything that is not advertising-related (i.e., if you send the identifierForAdvertising to your own servers even though you're not an advertising network or if you send the identifierForAdvertising in the same request with other data that could potentially identify an individual).
If my suspicion is correct, the advantage of identifierForVendor over identifierForAdvertising is that it won't get your app rejected.