Are you sure *all* directories and files in /usr belong to root?...
Here on 32bit all but /usr/local belong to root:root, while local and the dirs inside belong to root:staff (0 50).
...
... which unfortunatly isn't true:
#1
You won't be able to use mlocate as user until after you change owner and mod.
Note owner and SUID for group
$ dir -l /usr/bin/mlocate
-rwxr-sr-x 1 root mlocate 35816 Jun 13 2013 /usr/bin/mlocate
#2
chromium won't start anymore. When starting in VT you'll see that the chromium sandbox needs file mode bits different from what they are after you issued "chown -R root:root /usr/"
I can't await for more to come ... :-(
BTW: I won't mind if a mod moved this thread away from "upgrade-warnings", because it isn't and wasn't. And, again btw, this section should be called "dist-upgrade-warnings", you know why.