Congratulations! You've written a first draft of a science fiction or fantasy novel. You (and your heroes) have vanquished the enemy, and your story has come to a glorious end. And now, the real agony begins. Chances are your first draft is a misshapen wreck, which requires huge surgery.
The good news is, there's one great technique to diagnose and fix the problems with your novel draft. The bad news is, it's excruciatingly painful. But you wouldn't be doing this if you weren't a masochist in the first place.
That technique is: Try writing your whole novel over again, as a short story. From scratch, without looking at your novel draft. If possible, you can even do this a few times over, focusing on different POV characters or different themes.
This isn't the same thing as just writing a synopsis or outline of your novel, which is something you absolutely must do as well. When you're writing a novel synopsis or outline, you're not trying to make it a particularly great read on its own — especially not when you're doing it in the middle of the revision process. (Later on, when the novel is ostensibly done, you'll write a polished synopsis to show to agents and editors, but that's a ways off.) When you're writing a synopsis or outline, you're just trying to describe the main events that happen in your novel and how they (hopefully) fit together.
But trying to turn your already-finished novel into a short story is a very different process, akin to stuffing a reasonably tall adult into a baby carriage. Especially if you aim for the finished product to be not just coherent, but actually beautiful or a fun read. To do this, you have to pare away everything but the essence of your novel's story and then find a way to convey it all over again, using the elegant and shapely form of the short story.
Especially if you try your best to create an actual, readable piece of short fiction, you'll be trying to imagine the key points of your novel all over again. (And possibly generating some new images or bits of descriptive language that you'll find useful in a later draft of the book.) The change of format and the "starting from scratch" aspect both force you to re-engage with the story in its most basic form — and if there's something that's not clear to you off the top of your head, don't cheat and look back at your manuscript to see how you hand-waved it away last time.
But yes, this is a very, very unpleasant thing to do. Just trying to change gears enough to see your novel in this totally different way is likely to give you brain cramps, and the actual process will be like pulling your own teeth, then reinserting them, then pulling them again.
Why would you want to do this? There are a few reasons. For one thing, this allows you to see more clearly what the main arc of your story is. For another, it's a great way to make sure that the things you've decided are subplots are actually subplots — and that you haven't somehow elevated a subplot to "main plot" status while keeping the main plot squished into the space of a subplot. Paring away all the subplots, more or less completely, lets you see what's left. But most of all, this is a way to convince yourself that your protagonist(s) and your story are really epic and perfect as they are — and convincing yourself is half the battle, when it comes to revision.
Most of us at least try our hands at both novels and short stories, so you already know that novel-writing and short story-writing use very different muscles. Most good short stories really pursue one idea from beginning to end, setting up a conflict early in the story and resolving it (after a fashion) in the end. One reason why writing short stories is such a valuable undertaking, even for writers who mostly want to write novels, is that you get lots of practice writing beginnings and endings. But another reason is that short stories have to push on, relentlessly, from start to finish. This is true of the most leisurely "slice of life" story and the most action-packed thriller story. Novels can digress and explore side streets — short fiction has to be like a bullet train.
And rewriting your novel as a short story might let you see where you've papered over the cracks, in a way that a synopsis or outline might not. Sometimes your novel is going from A to D, skipping over B and C entirely, and you might not catch it in the revision process because it makes sense in your own head. Not to mention that there might actually be lapses in logic, where one character does something that makes no sense based on everything we've seen of him/her until now.
For bonus points, you can also try redoing your novel as a few different short stories — if you have more than one viewpoint character or protagonist, try writing the whole thing from just his or her point of view. Don't worry about the stuff he or she didn't personally witness, just focus on the story as this character experiences it. If your novel's in third person, you can try seeing what it looks like in first person, and that can help you get some more perspective. This can be a great tool for seeing if the whole thing actually makes sense from one particular character's point of view.
The biggest problem with revising a novel is the things you don't see. Your novel contains all your personal blindspots, as well as all the swerves and developments that you hypnotized yourself into seeing as totally plausible. You set out to write a novel about space marines fighting blobs from the future, but somehow you got sidetracked into mostly writing about the space marines' troubled relationship with the people who work in their cafeteria. (And that might actually be a better book, as long as you actually follow through.) There are lots of ways to discover the mistakes you didn't realize you were making, including getting feedback from friends and enemies. But this technique, of redoing it as a short story, is a pretty good one.
You might fail. Of course. You might try to redo your novel as a short story, get halfway through, and be unable to finish. You might even pile up half a dozen failed attempts to do justice to your brilliant novel in short story form. This is fine — in fact, failure can be as useful as success, with this technique. Chances are, you've still learned something about your novel by trying to reinvent it as a shorter, sleeker version. Each of those failures might hold crucial clues to your novel's ultimate success.