I agree with you that Hermione's character was indeed somewhat built up throughout the "Prisoner of Azkaban" movie at Ron's expense. Both Ron and Hermione exhibit tremendous loyalty to Harry in the books, and I do feel that Ron was a bit short-changed in the film. I've got loads of objections about the third movie, which you will undoubtedly run across in other threads, but admittedly, part of the apparent "decline of Ron" has to do with J.K. Rowling's plot and wasn't the fault of the director (if we are determined to pin blame, as I usually am

).
Ron wasn't part of a lot of the main action of the "Prisoner of Azkaban" book, and as we all know from watching three of the Harry Potter movies, the directors have a tendency to cut everything that is not main action. (This isn't entirely their fault, either! I'm trying to ward off all of the third film-defenders in advance because this is supposed to be a pro-PoA post.

) Due to her obviously crucial role in the whole Time-Turner sequence, Hermione was a very important character. She also has a lot of her good-little-girl-comes-out-of-her-shell-and-rebels moments in the "Prisoner of Azkaban" book (e.g. punching Malfoy, walking out of Trelawney's class, etc.), which the audience (including myself) loves and therefore end up in the final screenplay. Ron, unfortunately, does have a smaller role in the "Prisoner of Azkaban" book as well as in the movie (which greatly saddens me as well, because I too like Ron as much as it is possible to like a fictional character

).
You have to look at the other movies as well. Excluding the semi-peripheral member of the trio is not a new thing associated with either "Prisoner of Azkaban" or Cuaron. Columbus did the exact same thing with Hermione in "Chamber of Secrets." I mean, how could he have made her into a huge part if she was stuck in the hospital wing either petrified or as a cat throughout the majority of the plot? The same thing goes for Ron in "Prisoner of Azkaban." If you break your leg in the Shrieking Shack, you're probably going to get shafted in the Time-Turner sequence.
Now, I remember feeling the same way about the diminishing of Ron's character while watching the "Prisoner of Azkaban" movie for the first time, but I haven't watched the movie in over a week (

) so I might have to brush up on some of the finer points again. If your post is referring to other things in addition to the scenes of the book in which Ron is clearly absent, just remind me and I can assure you that I'll get back into my "anti-PoA mode" very quickly!

I really love ranting about the third movie...