It seems highly, highly likely that the update, which is only necessary for Wiis that play Metroid, is to enable the achievement tokens to be passed around through the message centre. (Read up on your Metroid previews if you have no idea what I'm talking about).
Since Metroid fans are the only one getting it, I'm assuming it's for Prime only online features, right?
Oh, and Super Paper Mario, which is famous for having an update on it, doesn't run an update screen if your Wii is up to date - so Metroid didn't just 'check' - it's for Metroid specifically. Unless Nintendo is going backwards with their system updates.