Let's start out by assuming you're not rich. Not many musicians are. While it would be just lovely to waltz into the shop, pull a custom Paul Reed Smith off the wall and plunk down your American Express Black card to cover the full sticker price, such things are a luxury more often afforded to the One Percent.
The alternative: pick out the perfect guitar and then go and find someone who doesn't want his anymore. It's not a pipedream, the used market for guitars is huge. But, while it's reasonable to consider a certain level of quality in an axe that just rolled off the assembly line, it's harder to predict the details of one that's been sitting in someone's spare bedroom for half a decade. The trick, then, is to ask just the right questions to ensure you're getting a quality specimen. And, while there are a million questions to ask, there's one in particular that strikes me as more important than the others:
How's the neck?
I think we can agree that every aspect of your new used guitar is important. My argument here isn't that you should care about the neck and ignore everything else, it's that, of all the things you might need to fix before the guitar becomes playable, the neck is very often the hardest, most expensive part to deal with.
If there's doubt in your mind, I suggest an experiment: call up a guitar repair shop and ask how much they charge repair or replace the bridge, volume knob, pickguard, pickups, tuners or input jack. Now ask them how much they charge to replace the frets, the nut or the truss rod. Ask them what they charge to plain the frets. Hell, ask them what it costs to replace a neck that's been so badly warped (I've seen it happen) that you simply cannot get a consistent tone or feel from one fret to the next. After they give you the price, tell them you forgot to mention it's a neck-through-body and then enjoy the maniacal cackling on the other end of the phone.
So, don't get, like, screwed.
The bottom line is, go ahead and get the guitar you've always wanted, even if it's not brand new. And further, go ahead and buy it online because it's cheaper, faster and more convenient. But do your homework and ask the right questions. Get pictures, get guarantees, and make sure you have recourse if your new twanger arrives in unplayable condition, requiring countless hours and dollars worth of repairs.
Or, better yet, don't let that happen in the first place.