I can see how it might seem a bit like making too fine a point, especially in these modern times, but Catholic guy and some of the "enlightened" gay characters were in the book from 15 years ago, when pedophile priests weren't all the rage they are these days, and homosexuality wasn't as talked about as it is now.
I also personally didn't feel that the final fight was Matrix-y, just slow motion and hyperreal.
Really liked the movie myself.