I have an Ibanez s521 and the harmonics (both natural and artificial) are very muted compared to other guitars in its price range. The guitar had a pro setup done and what not. I've played plenty of other guitars and I was always able to do easier harmonic, being an Ibanez you'd think it could squeel (well it can, but barely and unlike most you have to be exact exact with the thumb technique or it fails).

Is it most likely the pickups, or is it something tbat might be wrong with this specific guitar?
Well the inf pickups definitely leave alot to be desired, but I would adjust the pickup height first and see if that helps, they could be too far away(not picking up the natural harmonics well) or too close (the magnetic field is causing the strings to stop vibrating too quickly).

Also could have to do with your amp/pedal settings etc. When you say youve tried many other guitars and they are easier...have you tried these guitars on your rig?
not all guitars feel the same. the harmonics are naturally where they are, you just need to find them, and you will get used to them.

i only had that problem going from a Gibson LP to a Ibanez Prestige. different radius, neck, scale, and on and on and on. i got it down it just took a few hours.
The main reasons I have come across for poor harmonics are bad strings, bad setup, or just not being familiar with the guitar. Sometimes the harmonic isn't exactly over the fret. While some pickups can enhance certain harmonics if they are sounding muddled it is not likely the fault of the pickups.
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