In a recent hotfix, Blizzard has changed the rep gains from Throne of Thunder on Remix: Mists of Pandaria, making bosses award 1000 rep instead of 300.
With these changes, players can reach Exalted status with Shado-Pan Assault more than three times faster. Hotfixes don't show if the rep is now awarded daily or weekly, so we'll need official confirmation.
This change applies to all 13 bosses in Throne of Thunder.