Gibson's are most certainly NOT junk guitars. They make some fabulous instruments. Their quality control is spotty, but I actually like that in a manufacturer of that size. Their guitars are usually good, some times horrible, but occasionally amazing. If you are buying a Gibson, you need to spend a lot of time shopping for one of the great ones, but when you find it, it will be one of the best guitars you have ever played. The same can not be said for Fender, Martin, Taylor, or PRS. They all make guitars which are very consistent. They will all be very good, but you will rarely find one which is great.
Gibson is famous for having some of the purely cosmetic details be less than perfect. You will never find a Gibson which has binding which I would consider even close to acceptable, but I have a much different set of standards for my guitars. My guitars do not have the name Gibson on them, so I have to make a guitar which is perfect in all respects in order to get through to the customers. I don't really hold this against them either, because it is not a situation where they once did it right, and they stopped for some reason. They NEVER had perfect binding. But when they were developing their reputation, it was not an issue. I have seen Lloyd Loar era instruments, and they had many of the same issues that Gibsons have now (uneven binding, poorly leveled finish at the bindings, etc.). But no one cared back then, and Gibson is so hide bound (particularly after the mistakes of the Explorer, Flying V, and don't even mention the Modern), that it is not very easy to change things which are of purely cosmetic concern. Gibson is one of the few major manufactures who still uses nitrocellulose lacquer on all of their guitars for just this reason. Many companies use nitro on their high end instruments, but on the cheaper ones, they use cured polyesters. Gibson uses nitro, period. They have a very hard time changing, and they have for many years now.
They bind their necks that way because it is cheaper, but that doesn't mean it is worse, nor does it mean that some people don't prefer it. It is a major pain in the ass for repair, and a fret dress costs more because of it, but their are people who just have to have their "nubs" for the end of the frets. Myself, I just hate bound fingerboards. They are the primary cause of lifting fret ends (which causes buzzing on the "E" strings, and which catches the high "E" string at the most inconvenient times), they raise the cost of a refret by a lot, and if you don't keep your guitar in a well humidified environment, when the fingerboard shrinks, the frets will push right through the binding, and crack it. Bindings are a structurally really bad idea, but manufacturers do not make design decisions based on the long term health of the instrument. They are concerned with the salability of the instrument, not the long term stability. For instance, Taylor has always bound all of their fingerboards, even it only in ebony. They do this because it allowed them to avoid the drop off at the body with the old style necks, but with months the neck would have started to move, causing buzzing up around the body fret. But they sure looked great when you sited down the neck in the store (even though almost no one ever has an issue with that drop off in real life).
I could go on and on about the crappy fret work done in factories (ANY factory, none of them do it right), but why bother? Same with setups. If you buy a new guitar, it will not be setup right. Ever. Nothing is going to change that, though, as setup is so individual, and because factories primary concern is making sure it does not buzz (when most people pick up a guitar in a store, if it buzzes, they put it back down, and will not try it again, which makes them pretty hard to sell). All this means is that when you buy a new guitar, you need to budget $50-100 to get it setup. No big deal.
If you want a guitar that is perfect in all of the details, you need to go with a custom guitar. You will never get that from a factory guitar. That does not, however, mean that I think all people need custom guitars. You just need to be aware that factory guitars will have some (usually purely cosmetic) issues.
There was a thread recently in the mics forum (which I did not read) which asked, "Do you get what you pay for." The answer is almost always, yes. The trick to that answer, and which you need to understand, is that there is a diminishing rate of return. There is a noticeable difference between a $100 guitar and a $500 guitar. There is another big difference between a $500 guitar and a $1000 guitar. The difference between a $1000 guitar and a $2000 guitar is about the same as the last jump ($500 to $1000), but for double the price difference. The difference between a $2000 guitar and a $3000 guitar is pretty small, other than purely decorative stuff (pearl inlay and the like). The difference between a $3000 guitar and a $4000 guitar is going to be very small, and when you get into the price range above that, you are almost always talking about purely cosmetic (or psychological) issues. Inlay, fancy wood (Brazilian rosewood is a perfect example of psychological differences, since the stuff is totally without merit when you consider the quality of wood which we can get today). The other part of the equation with instruments of that price is the name attached to them. Jim Olson (who is THE biggest name in small shop acoustics these days) has a base price of $12,500. Are his guitars any better than the guys who charge $3000? Well, in some respects, yes. You will not find a guitar, anywhere, with the level of fit and finish that Jim's guitars have. However, they do not play any better, and they do not sound inherently better (you may prefer them, but that is another issue all together). They certainly are not four times as good. But they have Jim's name on them, and that is why he gets the prices he does. He used to have a base price of around $6000, but he was finishing guitars, and he would see them on eBay a week latter for double what he had charged. He (rightly) figured that was his money, so he upped his prices, and he still has a back log of eighteen months. He gets all of that because of his name (and the fact that James Taylor will never play another guitar in his life, and says so publicly on a regular basis).
So back to the question of Gibson. Why do they get the prices they do? Because they can. That is the same reason Jim gets the prices he gets, the same reason Fender gets the prices they do, and the same reason I get the prices I get. Because they can sell everything they make at that price. We all make fine guitars, and though there are differences in the fit and finish area, they all play and sound just fine. Different, but fine. Beyond that, it is all just a matter of what you like, and does it push your buttons. If you want to play southern rock, you sure as hell better get yourself a Gibson. If you want to sound like Clapton (shame on you for copying) you need to play a Strat. If you want to play country, you need a Tele. Beyond a certain point, it is all just a matter of preference.
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"Cowards can never be moral."
M.K. Gandhi