"The best writing is rewriting." ― E B White
An author and professor from UBC once told me that the worst writers in her classes were often the students who got straight As in high-school English. They were used to churning out tight essays in a single evening and ending up with perfect grades. However, first-draft essay mastery doesn't translate to fiction.
A large part of writing a first draft is discovery. Even if you start with plenty of research, character maps, and outlines, big-picture issues can creep into your manuscript when you are staring at it one page at a time. That's completely normal. Every writer should expect their early drafts to be full of problems, many of which they don't immediately see for themselves. Beta readers are crucial at this stage, and writers should always be prepared to make significant changes as they tidy up a novel's scaffolding.
How significant? This same author and UBC professor told me her award-winning novel, which is 200,000 words, took her about 600,000 words to get right. Similarly, my first manuscript (100,000 words) was a complete mess, so I set it aside and re-wrote the entire thing from scratch. That ended up being my MFA thesis project. Even still, several drafts later, I've decided to trash it one more time and start fresh. I tried to fit too many pieces into one story, so on the advice of my agent, I will next attempt to twist my concept into two or three novels.
Does this sound demoralizing? It's certainly not easy to turn your back on so many hours at the keyboard. However, nothing is lost. With every long writing session, you improve, the process becomes easier, and the story takes a sharper shape in your mind. Even a fully scrapped draft represents solid time you spent getting to know your world and characters.
A local theatre troop wrote a brilliant musical called Ride the Cyclone, which ended up on Broadway. A few years ago they held a fundraiser show in which they performed several numbers that had to be cut because they didn't end up fitting the story. This was an eye-opening experience for me. The songs they cut were amazing!
At the end of the day, the narrative must come first.