Since march 26, 2010 there is shared-mime-info 0.71-1ubuntu1 which recognizes the new mime type "video/mp2t" alias "mpeg 2 transport streams".
I am not sure if freedesktop.org is the right place for this report. But the affected package is desktop-file-utils. I found that "/usr/share/applications/defaults.list" is where the default application for a mime type is listed. Like "video/mpeg" I'd expect totem to play "video/mp2t" by default.
To coordinate all changes for video/mp2t I filed https://bugs.launchpad.net/ubuntu/+source/desktop-file-utils/+bug/552162.
Please report the bug to totem developers, in bugzilla.gnome.org.