It is more a matter of what rare disc people will count or care about than which game or disc or variation is actually the rarest.
What is the most ANY gamecube game has sold for? We are perhaps at the lowest point in terms of demand for the system that is just one generation old. Two generations from now perhaps games for the system will be where SNES is now. Only then will we know for sure if people are going to collect the system or if it will fall flat like some other systems have done.
Both Metorid and Zelda are available in different packaging so only someone trying to collect every varaitions will pay a premium. Well perhaps a few Zelda or Metorid collectors who must have everything will want it for the same reason. You really need a flock of buyers looking to complete the entire set AND for them to count it as one of the needed games for it to go anywhere. If the game is added to the require game list and everyone tries to track it down before it gets too hard to find then it WILL be hard to find and the price could go high but that is a ways away.
I am set up every year at CCAG and I am sure if you have been there you have seen me. I have a store on the easy side but live on the west.
Hey now that is an easy way to go. Even Pokemon box is eliminated that way as it was mail order. The majority of the retail games are R1s and R2s. It won't take you long to wrap up that set at all.