Here's what was up with that. (This is on the DVD extras in interviews.) Sachar realized, along with the director and who-all, that the role of Stanley was quite physically demanding. Ideally to stay true to the book, they'd have had to cast a young actor who was overweight and make him slim down and shoot all scenes in sequence, or have a slim actor bulk up and shoot in a reverse timeline. Owing to the ensemble cast's needs and such, shooting in sequence was not feasible and because of the difficult physical demands Sachar decided to discard Stanley's weight issue as a plot point. He did not sound, in the interviews, as if it was a casual decision for him, but he did think it would have made the creation of the film difficult if not impossible.

So if the issue of Stanley's weight rang especially key for the reader, I agree that that's going to bias a viewing of the film. Might make one think the translation of book to film failed. I felt much more at peace with it after I heard Sachar's interviews.