Nintendo has said that it will no longer publish the Wii bundle of the Metroid games suggesting instead that if you want the special edition, you go and dig around the trade-in shops.
In an email responding to why Metroid Prime: Trilogy couldn't be found on Amazon, Nintendo explained, "Unfortunately, Metroid Prime Trilogy is no longer being shipped. Having said that, you may be able to find what you seek through the secondhand video game market."
When pressed a little further, Nintendo added, "When first introduced, it was announced that there would be limited availability. However, a reason for this was not announced. That being said, you may still be able to locate a copy via stores that specialize in previously played or used games."
If you find one cheap, it may be worth picking up. NGamer loved it, "Aside from the controls, the GameCube titles benefit from Corruption's achievement system, which rewards you with medals for accomplishing certain tasks. You can swap them for unlockable items, including the option to save screenshots that can be emailed to your friends. All three games run at 480p in widescreen, so they've never looked better. Maybe this is what you've been waiting for..."