I haven't been tracking Pandaria that closely, but today's blue posts strike me as an obvious "did they REALLY not see that coming?" issue. For some reason, the current PVE justice point tier (obtained by puggable 5-man content and others) was offering item level 450 gear while the PVP honor tier (obtained via battlegrounds) was offering item level 464 gear.
Blizzard somehow thought that the PVP secondary stats on the PVP gear would make it unfavorable for use in PVE, but having it be an entire tier higher in base stats was apparently more than enough to offset this. And thus, players were farming battlegrounds - or even converting their justice points into honor points at a large loss to buy PVP gear instead. Blizzard will now be normalizing all the items into the middle of the road and adding some extra PVP stats to the PVP items to offset the lost stats.
I wonder what it was that made this so hard to foresee? The cardinal rule of MMO incentive design from the last eight years - and I've seen Ghostcrawler acknowledge this - is that you cannot change player preferences with incentives but you CAN and will change player behavior. Putting gear that is otherwise difficult to obtain on a PVP vendor is one of the most common ways to screw this one up. I recognize the desire to have the incentives be desirable to all players, but the impact of getting this particular one wrong is too great.