I have floundered a bit on my second novel and finally realized I did not have a central heartstring, a big question. I had the 'good guy' and the goals; I had antagonizing forces, but no big question to provide depth.
Actually, let's back up.
I started my second novel as a follow-on of the first. I wanted to follow the characters (heroes) that were established in the first novel, and I began 'discovering' them in a new story--the second story. The villain from the first novel was gone--he'd been vanquished at the end of (plotted) book one, although his organization was intact. For book two, I was keen to try this 'discovery thing' I keep hearing about. I allowed my established characters to do things. In different combinations, places, with their personal goals in mind. I thought i was on my way.
But the story stalled. I couldn't sort out why... Wasn't I discovery writing? Weren't the characters supposed to behave naturally and lead me toward something interesting?
I 'discovered' that I didn't have a villain. So I needed to build that, and I did. It was a breakthrough. New villainous character, with goals, and this immediately added depth.
Now we're caught up, and I bet this point is where you are.
So I kept discovery writing, happily working the villain and his goals into the story, too. Discover, discover, no idea of where these characters are going, but everything I have heard is that discovery writing is more natural and engaging than plot-heavy novels. Write, write, write.
I stalled again. This time, I realized there was no big question at the book's heart. There was no joie de libre in the novel, nothing to make it resonate, or matter, to anyone in the world. What is the crux of this story? Why must it exist? (Obviously, it doesn't 'must exist.') I don't want to write an entire novel unless it has a reason to exist... that feels personally meaningful to me.
And so, I mulled and thought and played with ideas, and during this stall, I asked how my characters were approaching their own personal goals. How is Character A trying to get where he wants to be? Character B? The villain? The secondary characters? What are the devices and interactions and behaviors that each character uses toward their own goal? (All of this, by the way, was discovered in writing.)
I discovered (heh) that my characters have different personalities and strategies. Each uses a different approach within their own life. And based on that, I was able to formulate what the central crux, the question, the 'moral thing' is of this particular piece. In my case, and for this novel, that central bit is the question: 'are we more effective as individual agents toward a personal goal, unencumbered by others, or are we more effective as a group, in concert, working toward a shared goal?'
This is resonant to me, it 'matters,' because of the failed 'stronger together' campaign of a recent presidential candidate and the current power structure of the US victor, who based a campaign on chaos. In other words, it resonates with me to ponder whether cooperative effort is truly more effective than individual determination-at-any-cost.
My characters naturally drift toward isolation, or alternatively cooperation in their goals. Who will win in my novel? The villain? hero A? Hero B? I'm not sure, but it'll come.
To answer your question, I believe you'll be happier when you identify a central question, thrust, moral, what-have-you that complements and deepens the conflicts that you've already placed in your story. And I found mine through examining my characters' choices and behaviors--and once found, I accentuate the theme to give my 'discovered' story more cohesion.
My answer is to examine your characters. Find something that runs through your story. Something that resonates with you. Is it the role of gender? The various faces of power? Nature vs. nurture?
Your central heartstring can be anything like this, find it, and I think that a novel that has this, in addition to the other stuff (goals and conflicts and antagonists and protagonists) is often more satisfying. Go for it.