Is it just me or are some GameCube titles rare? I was looking for the following but could not find them in (used) gameshops: Bio Hazard 2 Sonic Adventure 2 Battle Sonic Gems Collection Metal Gear Solid: Twin Snakes Super Puzzle Bobble All-Stars I tried all the major shops in Akiba, Nakano and Shinjuku but found none of the above. They seem pretty high profile to me. Did they get a low print or something?
GC games are very sought after in Japan due to the dull Wii soft output for hardcore gamers. Every Wii owner who likes to play games instead of dull kiddie shit comes to the point that he recognizes the GC is a reliable source for quality games that the Wii just can't provide in a similar quantity. Did you try the major SoftMap stores? They sometimes have more "last gen" than the big retro shops. Anyway, good Gamecube software is rather hard to get in Japan due to mentioned reasons. I had to buy each game I own seperately as there are just no good bundles up on yahoo, unlike almost any other "unpopular" console including Neo Geo and 32X. A pain in the ass indeed, but games & package design are so lovely that I think they're worth the hunt.
You're right that the GC was never a popular system to buy used games for, but the used market definitely did not improve with the Wii's lack of core-gamer support.