I had heard that the reason why they discontinued it was because they were anticipating the big crowds for Transformers. The theory was that with the AYCE pass, Guests were staying at the tables longer than Guests without the pass since they could get unlimited food (by going back through the line each time). Since they were expecting a lot of Guests to show up over the summer to experience Transformers (which did happen), they decided it would be critical to have the turnover rate of tables around the park to be as quick as possible in order to meet the demands of the Guests.
This is only what I heard- when they discountinued the AYCE pass, I asked a cashier at the Jurassic Cafe why the park decided to do that, and that was the explanation I got. Maybe someone can confirm this?
Of course, I'm sure money was a motive too. I'm an AP, and I would get the AYCE pass almost everytime I went just for the convenience of being able to eat as much as I wanted to throughout the day, so I ended up saving money each time compared to what all the food I ate would have cost a la carte. I do hope they eventually bring it back though! Something similar to Six Flags Magic Mountain's new AYCE season pass would be a nice add-on for APs.