Well, if I had a game store you might find a similar situation.
Think of it this way. What makes a good game store "good"? Prices? Sure, good prices are nice, but they aren't much use without stock. Nobody wants 50 copies of GTA3 for PS2 or whatever the last Madden game is. So in order to make your store seem awesome you have to have some cool shit in stock. The problem with this is that there isn't an infinite supply of cool shit. So you put out a bunch of PCE stuff at fair prices, all the shit sells, and now all you have is 136 copies of NBA Live 2002. You have to charge so much money that its worth it to lose the trophy game. If it never sells, its OK, since your bread and butter will always be reselling the most recent Halo or Resident Evil garbage, and there is an endless supply of that shite. Most people just want Halo or Street Fighter IV, and they can buy that anywhere, but those Neo Geo carts and Game and Watches and Vectrex units are the difference between that store and the local Software Ect or Best Buy.
There are other possible explanations. Keep in mind that eBay goes both ways. Why buy locally for over eBay prices? That's a good question. By why would anyone trade anything in for less than eBay prices? And if the store has to pay eBay prices just to get the shit, they obviously have to charge more than eBay prices when they sell it. Another explanation is that maybe nobody is actually expected to pay that much. Many stores give more in trade in than they give in cash. They say they want $1000 for something, but they'll probably sell it for $750 in cash, or $1000 in trade in. I've worked at a game store and I can tell you the best customers are the ones who buy 100 games a year but only have maybe one or two of those games next year. Their collections are in constant flux, and you profit from every transaction.
Semi-related: its important to keep in mind that while some people give good deals, some people gouge, etc, everyone who buys 20 year old games and then never sells them on to anyone (ie: myself) is part of the problem of rising prices. Every game that's in my collection represents one less copy of that game in circulation, and a minute price increase. The reason why they didn't make very many copies of Order of the Griffen is because in 1993 nobody f*cking wanted it. Now that the TG-16 is a legend we have people who weren't even born when the game game out looking for their copy. We've learned that most of these nouveau hardcore eventually lose interest and dump all their shit onto the next idiot, but some don't, and the supply just keeps getting tighter.
There will always be enough copies of Bravoman though.