I'm not sure either. It's probably mostly due to the scarcity.
Historically though, other versions of Marvel Vs Capcom 2 have consistently been sought after. I remember that the Xbox and PS2 versions were always relatively expensive in the aftermarket. Even the Dreamcast version seemed to fetch above average sums regularly years after it released. So maybe its history as a collectable game has lead some to believe that the ps3 retail pack is worth the money.
Here are current auctions for the ps3 version. All sellers are asking from $200-$300:
http://shop.ebay.com/i.html?_nkw=mar....c0.m270.l1313