One thing I found on my Ender 3 was that the Y axis belt must be very tight , and the table to crossrail bushings adjusted for zero play, or my Y dimension tolerances were off on the finished parts.
A good nozzle is also important, they do not last forever.
By far the biggest variable though is filament quality. PLA even from same maker varies a lot roll to roll and some colours print BADLY where other colours print fine. The ProPLA rather than generic PLA seems better. Not sure why, whether it is made with better resin or less fillers or ?.
I usually design part to part fits with some extra clearance so there is minimal filing and sanding. For under $300 CDN the Ender 3 has done an fantastic job for me, with minimal tweaks. However, it is not a $150,000 commercial FDM machine or a $500,000 SLA machine, and I don't expect tolerances as found in those machines from my $300 one.