That's my main gripe, if you have multiple email addresses that feed into one account, and like to email out from a variety of addresses its ugly. Really really ugly. Mainly because iCloud hates you sending a message that doesn't appear as an apple address.
If IOS 6 is better than 5 in regard to initial Apple ID I couldnt really judge as most my settings carried over from my ios5 install, thankfully, but iTunes Match lost its setup, and home sharing too and the remote app is now broken for me on iPhone.
However if setting up a new device has been improved/fixed. THANK YOU.