The upgrade wizard did the installation of XGL.

I never had XGL on my Ubuntu before.

After the upgrade, I rebooted, and as it did, used Xgl as default.

Maybe because it probed for a video card and found one, but not
blacklisting it, therefore enabling Xgl by default.

Maybe you could use a wrapper script similar to the compiz wrapper script to 
run Xgl?
(Like running compiz, if it doesn't work, start metacity, but in Xgl case,
run Xgl :1, if it doesn't work, continue bootup of GNOME/KDE on the Xorg server)

-- 
Xgl should be not run if card is blacklisted
https://bugs.launchpad.net/bugs/177062
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