Q: The humbucking neck pickup on my guitar always sounds too dark and muddy. What can I do to make it sound better?
A: There is always the option of swapping out the pickup for a new one that offers the response you prefer.
However, before doing that, try this: Instead of setting your overall tone using your bridge pickup (which is the way most of us default to doing it), use the neck pickup. Set up your amp and effects so that the neck pickup sounds the way you desire. This will probably involve turning up the treble and maybe turning down the gain and the bass. Now switch to the guitar’s bridge pickup. It will probably sound thin and too bright. But before you reach for the tone and gain controls on your amp, use your guitar’s tone control to pull back the high end a bit.
You may find that using this approach allows you to get a better neck pickup sound, then balance the bridge pickup against it with equally good tone.