Never mind that we don't know how much a Nintendo 3DS game costs to buy, developers need to develop the games first. And that costs money.
According to Harvest Moon publisher Marvelous Entertainment, Nintendo 3DS games cost - depending on the title - between ¥70 million ($840,000) at minimum and ¥100 million ($1.2 million) at max. These, of course, are projections Marvelous made, and actually 3DS development costs are expected to vary by title and studio.
Earlier this year, Marvelous Entertainment stated it would not be developing original games for the time being, but is focusing on established series.
The company's estimates are bound to drop over time as developers get better at making 3DS games and are lower than the average PS3 or Xbox 360 retail titles, but higher than the ¥40,000,000 ($480,000) for development costs for the Nintendo DS. Nintendo 3DS titles also require bigger teams and more time than DS games. Those better graphics don't come from thin air!