As an English teacher, I have read and taught much great literature. I have a stack of great writing to draw from when writing my own stories. What makes these writers great is their ability to write organically unified text.
A novel has organic unity not just when the story is well conceived, but when all the parts (characters, sub-plots, symbolism, descriptions, tone) mesh well and support the overarching author's purpose. I have put together a checklist for novelists who would like to give their novels that special quality. If you can accomplish organic unity, it will cause the reader to feel as if they are no longer reading some dime-store novel or a flash-in-the-pan writer-of-the-month but someone who has a universal message and a lasting voice.
1. Why Are You Writing This? - Every writer has a purpose. If your purpose is to get rich then you are in the wrong field. Think about why you are writing the story you are bleeding out through the keyboard (or legal pad). Is this story being written because you have always loved Tolkien and desperately want to write like him? Those people are like Willy Loman. "A dime a dozen". What do you have to say about life that is big news to everyone? Is there a problem with society that forces you to wake up in the night and yearn to do something about it? I have my personal soapbox. I won't write about it in this forum because I do a better job when I am weaving it into my narrative. Suffice it to say, my soapbox is a big one, I care very much about it, it has to do with changing things and I feel very strongly about it. That is what you need. Find that one hot button and press the devil out of it.
2. Blueprints - Outline your novel. I cannot stress enough the importance of this structural necessity. I spend more time researching and outlining my novels than writing them. An outline allows time for me to create deep, meaningful characters that have symbolic quirks, allegorical backstories, driven purposes in life, and even physical characteristics that lead the reader back to my overall purpose. I have time to create settings that breathe with my purpose or "soap box" ideas. I illustrate entire episodes where my purpose is flowing out to the reader through nuances they may never notice at first glance. I create all the seed ideas ahead of time so that when I am writing them they germinate into full blooming plants of meaningful and challenging ideas.
3. Read - I think it is highly important to read classical literature. Mark Twain once said that "Classics are books that everyone talks about but have never read." This is a true statement, but if more writers read classical literature, monuments to the craft, they would then emulate that craft in their own writing. How many times have I read a Charles Portis or Hemingway or Faulkner or Shakespearean line and thought to myself: "What was going on in that person's head when they wrote that?" I am amazed by the wordsmiths of the past. If you want to see some modern examples of people who write this way, check out Neal Stephenson, Martin Amis, Robert Heinlein, Isaac Asimov, Cornelia Funke or Joyce Carol Oates. These people care very much about the voice they have and actually weave with words something other than "Harry Potter is a good wizard and has a destiny".
4. Care - If you don't care about your characters like you would your children (even if you kill them off now and again) and you don't care about the story you are telling, then neither will your readers. I have edited through several short stories where it is obvious that the writer only created the plot because they "saw a really cool Stargate episode on Netflix last night" and wanted to explore another idea that the writer didn't choose to write about. I have news for you: they probably didn't for a good reason. I wrote a novella about a young man who goes to his grandfather's funeral and is reminded through flashback stories about the experiences he had as a boy on the farm and the lessons he learned from his sagely old patriarch. The problem was that nobody but myself and my family "got it". It was a memoir (basically) with a plot thrown in. I will revisit that novella one day when I care enough about it. Maybe I will when I'm gray headed and much wiser. There is much to explore within its pages that I have not lived enough to think about. Right now I care about This Broken Earth (my current novel) and have a soapbox to stand upon that is poignant, is satirical of current trends and is something that needs to be said.
5. The Market - Above all, make sure that your current soap box is firmly stamped with current trends in mind. I'm not saying go down to the local book store and see what is selling and then write copies of that. What is good for Amanda Hawking is not necessarily good for everyone. If all of us write supernatural romance then it would be a dull world indeed. I am simply saying that writers should be mindful of popular trends and try to find their own take on those trends while still staying true to themselves and their personal "soap box". I'm doing this (I feel) with my current novel, and still remaining true to my own high standards while listening intently to my target audience who have responded well to rough drafts of sample chapters. I also listen closely to their criticism and what they would like to read about along the lines of my themes.
You may never be a best seller, but if you write a good novel with all the elements balanced well, you will have something of which you can be proud. Who cares if they don't see everything you wove into its pages. When they do, it's fun to giggle and say "oh, I didn't think about that" as if someone other than you did it.
Revel in that.