Pickups that have strong magnets can effect string vibration if too close to the string, costing sustain. My setups have the bridge pickup furthur away from the strings on the higher string side and closer to the lows. Opposite for the neck pickup, plus I angle them.....
Sometimes pickups (humbuckers) can be improperly angled (both "bobbins" are not parallel to the strings when looking down from the side). Even angled mounting rings may not be enough. When this is the case, I make a VERY slight bend in the height adjustment bolts about 1/2" away from the head. This provides added "tilt" to level the pickup with the strings or angle it away for whatever sound you want. This way you don't have to screw the poll pieces way out, which can catch strings, picks, fingers, etc.
You'll find changing these angles will provide better harmonics and a more balanced output accross the strings.
I once thought a "Sweeping Arpeggio" was an Italian janitor.