Developer Retro Studios confirmed that save files from Metroid Prime 3: Corruption will remain incompatible with the forthcoming space bounty hunter epic Metroid Prime Trilogy.
The studio had this to say:
Due to the way the game data is allocated for production and the changes that we made in the source code, we were unfortunately unable to carry over the save file compatibility from MP3 to Trilogy.
It might seem like terrible news, but Corruption is one of the highest rated games on the Wii so you shouldn't really be bothered about playing through it again.
However, a surprisingly large portion of Wii owners asked whether Trilogy allowed save data from Corruption to be carried onto the new disc, and have anxiously been awaiting the answer. They won't be pleased.
Looks like you'll have to play through one of the Wii's greatest titles again to fully complete Trilogy. Such a shame.