Note: This also applies to Satisfactory.
In any Factorio play-through, you’re almost guaranteed to build something that is a mess, no matter how good your intentions are. Before you know it, you’ll have mess of belts and power lines criss-crossing each other with no apparent structure.
There are two reasons why a mess happens:
There is a resource (power or a constructed part) that you need right now before you can continue. You’ll end up creating a small quick-and-dirty factory setup, somewhere off the side, that creates that resource.
An existing factory setup isn’t able to produce resources to keep up with the demand. You’ll shoe-horn in more assemblers and belts, and in the process you’ll make the layout of that existing factory setup worse.
Once the mess is too big, you have two choices:
You can start a new game. This doesn’t really solve the problem, because you will run into the same problem again in your new game.
You can refactor.
Refactoring is the only sustainable choice. If you start a new game every time you have created a mess, you’ll likely end up abandoning Factorio altogether.
Refactoring in Factorio is generally easy. There usually is little preventing you from wiping out an entire part of a factory and starting over. The only exception is the infrastructure that keeps the hostile alien lifeforms at bay — you’ll have to be more careful to keep that running.
As for how to refactor… that’s another story.