If I remember correctly they said that they weren't going to inclued trophies because Sony (now) requires that trophies be on the game disks when they are initially shipped and if they included trophies then they could not update them when they update the game. They believed this would upset PS3 users because they might feel like they were being cheated.
"Some gamers might be wondering about PS3 trophies for ARR. Unfortunately Sony requires that the trophy lists be set once the master disk is submitted, and so they would be forced to wait for the next expansion to add more trophies to the game. This isn't acceptable for Yoshida-san; he instead wants to create in-game achievements that will let players show off their accomplishments." Link