Basically, at the start of each daily day, you have the choice between PvE and PvP dailies.
The PvE dailies put you against the forces of the Zandalari and the Mogu.
The rewards for a day are 60 valor, 24 Lesser Coins of the Elder and 1850 Kirin'Tor/Sunreaver rep.
The PvP dailies put you against Alliance/Horde NPCs and opposing players. You are forcefully flagged while doing these dailies.
The rewards for a day are 525 Honor, 50 Conquest, 16 Lesser Coins of the Elder and 1250 Kirin'Tor Sunreaver rep.
Note that this is only the setup for stage 1 of the Isle of Thunder and further stages may have different rewards/daily types.