I'm currently smack dab in the middle of my current WIP, and it usually takes this long to figure out exactly what the theme of the book might be. I know. I should have a theme when I begin, but as I have found out, the purpose behind every novel shifts and changes as it is written.
The current WIP has gone through several changes of purpose:
First, it was driven by a desire to write a story much like that of Pines by Blake Crouch. I was so fascinated with the way that Crouch was able to unveil one plot point at a time, fooling me into thinking I was in a small town when really I was not, and in the end shocking me with a fantastic science fiction story about the human propensity to pollute and destroy their environment.
Second, I began to become obsessed with creating a puzzle for the reader to solve. I wanted to go beyond what Crouch did and design a conundrum that was full of red herrings that all seemed plausible and in the process of that began to worry.
Third, I worried about the book having some type of spiritual message, fretting over the fact that I have set myself up as a Christian writer. The book is rather dark, as is, and is very frightening to read in places. I started to think that the book was about wasted chances, bad choices, and how we all would love to time travel and change some things about ourselves.
Fourth, I rested in the fact that as a Christian writer those themes usually rise out of me without much conscious effort. I write about what I know, and ultimately I decided that the book should first and foremost be a great story and that all the thematic stuff would float to the surface eventually, most likely in the revision.
So now I'm happily writing away at this thing. I have an outline, I can really see my characters and most importantly hear them, the framework in which my characters live is realistic and has all the kinks worked out, and my main character is lovable just enough that you'd have trouble firing him if he worked for you and did something crass.
I suppose it is all working out.
So what is the core of any novel? It is the novel's ability to engage the reader. Who cares about the theme, really. That will be something that is of a multiple nature if it is truly good writing. My students were once challenged to find multiple themes in a short story that was less than a page in length. They found 21 separate themes.
Make sure you have an engaging story. The rest will fall into place.