With a commit made to the GNOME Settings Daemon at the beginning of the month, middle-click paste support was disabled by default. This middle-click paste handling was disabled so that GNOME instead could use the mouse middle-click button for start selections and providing contextual menus (word definitions, sharing, and other tasks).
The GNOME developers laid out their contextual menu plans to be activated by the middle-click button on this GNOME.org Wiki page. However, not all GNOME users are happy with this change as Linux users have long been accustomed to being able to use the middle-click button for pasting.
With this Git commit from a few days ago, Red Hat's Matthias Clasen has reverted the change for this current GNOME 3.10 development cycle. He noted, "We're not really ready for this change, and we haven't messaged it properly. After discussion with Allan Day and Jakup Steiner, we'll defer this change until the next cycle."
So for GNOME 3.10 you will still be able to middle-click paste, but it looks like that will change with GNOME 3.12 in early 2014.