Since I don't get to the high-class stores all that often, most of the music stores I frequent are small-town operations. I start by scanning the room, looking for something that isn't like everything else there--cause they mostly keep stocked by dealing with primarily one company that ships them a lot of low-to-medium priced ho-hummers.I look for the trades and consignments. I might sight down the neck first, discard if warped or too bowed. Or I might just play something, with a flatpick. I'm looking for a warm sound that doesn't resemble the tonal vibrations of a garbage can lid, and is playable in tune up the neck.
If it passes that (maybe 25% do), further inspection is warranted. Unrepaired cracks, repaired cracks, worn frets , buzzes and rattles, and do the tuners work smoothly and hold adequately?
And finally, onboard electronics? It's a bonus if there's usable ones on a moderate-priced guitar. If it's a really good guitar, it's less of a factor--going to want to customize that anyway.
W-O