Comment 6 for bug 1020759

http://cgit.freedesktop.org/udisks/commit/?id=9541a638ffd is an interesting and hint why this was done: In a multi-seat scenario it is more robust to mount them below a per-user directory so that devices from different users are less likely to collide on identical label names. This also shields mounts from different users from each other, which looks like a security measure. Apparently it can be changed to the old behaviour by udev-tagging devices with ID_SEAT=all, though.

As for the /media -> /run/media change, I presume this was done to avoid having to clean up stale mount point directories after reboot?