Note: the crafting materials go for 9-10$ or so, even the bad ones, and take 7 materials to craft, so that material card is worth about 1.25$ on average. The loot cards also are worth a bunch and show up regularly. This takes away from minis value on the secondary market. You get more for your booster (which is worth, what, 10-12$ retail, unless you like paying through the nose by buying them individually instead of by the case) than just the minis' worth.
I don't think the prices are so much in the crapper. There's no economic model under which the rares are worth more than a couple bucks while some epics are worth 40+$ (like Vashj). In Magic you also get a whole lot of worthless boosters, since unless you open a money rare you might as well have opened nothing (we used to just dump our commons in a pile after drafts for the kiddos to sift through).
I'm sure if you totalled out the average value of the content of a booster, it would be slightly above what retailers have to pay for them. There has never been a game where a booster was worth less than its average content. When that happens, the price of boosters go up or availability dries up... See From the Vault series for an example, when it comes to non-blind content, but it's the same principle really. If your store made more money out of singles than boosters, they'd open up all their boosters to sell as singles until the prices went down under the booster prices or they ran out of boosters.
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