Ah ok, I know that older Wii's have problems reading dual layered discs (which Metroid Prime Trilogy is) and thought it was related. Sucks though that the game probably won't sell and the case will most likely go in the garbage 
But good luck on the hunt
I loved the first 2 prime games and have yet to play the 3rd.
The 3rd is really the best IMO. Totally worth it!
My launch Wii has never had an issue with dual layer, it has had issues with MPT

The reason that I know it's not a DL issue is that my backup plays just fine. If the Wii were going to have a hard time reading anything, then a DL DVD-R would be it.
I know certain Wii systems have trouble reading the Dual Layer games.
My theory is this is the reason why production for the game was abruptly stopped. Nintendo never said why. As far as I can tell it was never meant to be a limited edition type thing.
I remember reading that this game and Smash Bros. couldn't be read by older Wiis. Pretty sure Smash Bros. was re-released on a single-layer disk.
Based on what I've experienced, I can't help but think you may be right on this one.