To be fair, the only reason Dragonball GT: Final Bout plummeted in price is because Atari rereleased the game when the PSX was on it's death bed. People finally had the opportunity to play the game and when they realized how abysmal it was lost interest immediately.
But your point is valid. Just look at the Gamecube. The games that seem to retain their value are the "big" first party titles and a few other popular ones. Clearly nobody is having trouble finding Super Smash Bros. Melee but it still fetches a decent price.
I firmly believe the days when the late gen RPG or quirky Japanese game are the "rare + money" games are over. Maybe a handful will sneak in since the PS2 has been steadily seeing oddball releases that may or may not be both decent and in short supply but, for the most part, we aren't going to see another Panzer Dragoon Saga. Print runs are too big and quality games get too much attention these days. These days it seems that rare games will be made by accident like what happened with NCAA College Basketball 2k3 on the GCN. So while everybody will be looking at the newest Atlus release as a potential rarity they might be looking in the wrong direction.
What I can see happening on the Wii is a situation where a genuinely good game gets lost in the sea of shovelware and is only rediscovered by the masses much later on when copies are harder to come by. Something similar happened to Eternal Darkness on the GCN. At one point it was selling brand new for $12 before people figured out how awesome it was. A situation like this won't make a game rare but it will increase its value. I think Blast Works is a possible contender for that. I would have skipped it if I weren't tipped off by a friend. At first glance it looks no different than the rest of the generic software it sits next to on the shelf.