I think, in part, this may have been because I was trying to do too much. I had multiple POV characters - one of which was a child - and was trying to tackle themes like faith vs. reason. I can also see now that I didn't clearly identify what was at stake for my characters.
In hopes of learning how to edit my novel, over the summer I read Scene & Structure by Jack Bickham. If you haven't read this book yet, I would highly recommend it. After reading it, I decided that if I am going to keep writing, I better learn how to tell a story. For now, I think this means putting that other story aside, and trying something simpler. I've started another story - one with just one POV character, and, as I write, I am trying to stick fairly closely to the principles I learned from Scene & Structure.
To summarize, Bickham states that there are essentially 2 components to a story - scene, or the part where something happens, and structure, the part where the character reflects on what has happened. According to Bickham, scene and structure usually play out in the following pattern: