When asked about the issue on the beta forums, Ghostcrawler offered a pretty reasoned explanation for the change. He says that most quests with green rewards will only give you one choice (that matches your current spec). However, there'll also be vendors in every zone from whom you can buy sets of gear that aren't quite up to the item level of quest rewards in that zone, so you can fill in itemization holes or help bolster an off spec a little more. Quests that offer blue rewards will usually offer rewards for any spec your class can be, giving you some flexibility when it comes to rare rewards. Also, Mists of Pandaria questing is more non-linear than Cataclysm's, so you'll be able to hit up a different zone in the event that you need gear for a specific level range.
Ghostcrawler's full response (and an image of one of the vendors) is after the break.
Filed under: Mists of Pandaria