I doubt that Corruption sold "poorly" due to too much scanning and backtracking. Those elements are what fans of the Prime series loved. New people wouldn't have been familiar with it one way or the other in advance.
More, I think it's due to Wii sales of "hardcore" looking games are unpredictable even when they're published by Nintendo and part of a storied franchise. People seem to forget what the attitude on the street was surrounding the Wii in the first year after launch. I know of many Gamecube owners and Nintendo fans who refused to buy a Wii because Nintendo "betrayed them with teh casualz". The Wii seriously broke Nintendo's core base; it took Mario Galaxy to drag those people on to the Wii at all, and even then, most of them just played Galaxy then sold the Wii or put it in the closet. (Spoiler alert: Nintendo's own capricious, bitter, hardcore fans can be their worst enemy.)
To the largely new, expanded audience Wii owners meanwhile, Metroid Prime 3 probably just looked like another one of those Boy's Games with some Space Robot Person on the cover shooting aliens. Why would they give the game a chance, even if it wound up being a good game? Fans can't seem to get it through their heads that Metroid has never been a widely popular serious - only deeply popular with hardcore Nintendo fans. Corruption selling 1.5 million makes it pretty decent by the standards of past games in the series - only Metroid Prime 1, to date, has been the breakout title. it even odds to date that half the reason why it sold what it did on GC was because tons of people thought it was Nintendo's Halo, and bought it because they could finally have an alien killing FPS on their Gamecube.
