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That said, cheaper stock guitars often have absolutely horrid pickups. Swapping the pickups for high-grade models is often the first modification to do on a guitar. This makes gauging the tone of a stock guitar rather difficult. Maybe it sounds too dark or bright, but is that because of the guitar or because of the stock pickups? This is where a little internet research comes in handy. Pickups cover a wide range, and I would expect most guitars can be made to sound how you like them given a carefully-thought-out pickup swap.
== Electronics ==
Most guitars come with 2 knobs for volume and tone. Note that turning down the Volume knob actually affects tone as well usually - without a "treble-bleed" circuit in the electronics, turning down volume actually rolls off some high-frequencies, similar to turning the Tone knob down slightly. To get an accurate gauge of the guitar's sound, make sure you turn both of these all the way up. Try adjusting them when you play as well to make sure nothing fishy is happening. Sometimes dust can get in there, which sounds scratchy as you turn the knob - this can be alleviated by turning the knob vigorously back and forth about 20-40 times, blowing it out with compressed air, or simply replacing the potentiometer.
Some guitars have more knobs - sometimes this is for independent volume/tone control of each pickup. If unsure what the controls do, consult a salesperson or the internet. Sometimes a guitar will sound horrible, but it's because it has some special electronics that really should never be used because it was designed by an idiot.
Be sure to give the pickup selector switch a good workout. Make sure it is easy to use and doesn't slip off the desired setting or stick in dead-zones between settings.
Sometimes a guitar will have pops and crackles, or the signal just sounds weak or noisy. Sounds like a bad soldering job in the electronics. But before blaming the guitar, try a different cable, or the same cable on another guitar. Cables tend not to last and are usually the problem.
Cheap guitars are often not shielded properly. All the cavities where the pickups and electronics reside should be covered in conductive tape or paint to shield them from external interference. This is most clearly heard as noise, loud hum, and out-of-tune radio noises. If you can hear actual radio stations or phone calls, that sucker ain't shielded properly. It is particularly evident as hum when near flourescent lights. It's not too complex to shield an unshielded guitar, but it can be a pain in the ass. If there's a better option on the shelves, just go with that. Note, single coil pickups tend to hum by nature, so a little hum on single coils doesn't necessarily reflect a shielding issue.
Some guitar use active pickups or other electronics, which require battery power. As this battery becomes weak, the electronics will begin to malfunction. I can assure you very few music stores actually replace these batteries. I recommend avoiding active pickups or other such electronics anyway. However, if you have done some research and are dead-set on actives, make sure the guitar has a fresh battery for a serious demo. Again, if the tone sounds problematic and you are intent on a purchase, a salesperson should be happy to replace the battery, which takes about 5 minutes tops.
== Aesthetics ==