When you’re having your guitar or bass set up, with the action and intonation adjusted all ship-shape, don’t forget to take a look at pickup height.
Like action, pickup height is a personal preference (unlike intonation, which is an exact science), but guitars and basses do have an optimal pickup height that produces the best tone (usually specified in their owner’s manuals and on their manufacturer’s websites). You don’t want the pickups too far from or too close to the strings, and you might find that your instrument really “comes to life” when just the right pickup height is achieved.
You just have to take some time and experiment a little. Fender and many other manufacturers specify standard factory pickup height settings for various instruments (and recommended methods for measuring it; note in the photo at upper right that the height of the bass side of a Jazz Bass middle pickup is being measured with the low E string fretted at the last fret), and these make a good starting point. There are no hard and fast rules; you just have to raise and lower both ends of your pickups until you find the tone you like best.
It’s usually a pretty simple adjustment by means of height screws on either side of each pickup. Besides the right screwdriver, a good tool to use is a ruler with 1/32” or even 1/64” increments that let you accurately note various pickup height measurements and preferences.