If you open an Xcode 4.x project at Xcode 5 and then open a xib at Interface Builder, you will get an alert:
I have tried the above solutions, but as other users pointed out, didn't seem to work well... Strangely, after downloading Cocktail for Mac, and cleaning up broken preference as well as caches and other junk (which I did just to maintain my aging Mac) the "Always Upgrade" mistake was finally fixed!!
I haven't bought cocktail, honestly, you can use it for free for ten launches or something. So, you can go ahead and get your Mac cleaned up and fix that burden along the way.
I modified the Dave DeLong's command to reset the "Always upgrade". Try it.
defaults write com.apple.dt.xcode IBAlwaysUpgradeAutolayoutDocuments -boolean false
I didn't have luck with either of these commands, but this one worked for me...
defaults write com.apple.dt.xcode IBAlwaysUpgradeAutolayoutDocuments -int 0
In the File Inspector for the xib (cmd-opt-1), you can change the "Opens in" popup to say "Xcode 4.6". This will revert the document format to one that is compatible with Xcode 4.6, but it also means you will not be able to take advantage of some of the new capabilities in Xcode with regards to xibs.
If you want to "reset" the "Always upgrade" choice you made, you can do that by resetting that particular user default using Terminal:
defaults write com.apple.dt.xcode IBAlwaysUpgradeAutolayoutDocuments -bool false