Why do people constantly dog on Metroid Prime's sales? The Prime games sold on par with the rest of the series, and Prime 1 is the best-selling game in the series. It may very well lose that crown to Prime 3 eventually. Sales are fine.
Prime 2 is the weak link there, sales-wise, but that's more the Gamecube and Nintendo's fault than the game's (best of the 3, in my book); Nintendo had driven away the mature and hardcore demographics as best they could by that point. When Prime 1 came out, they still mostly appeared to be trying to throw off the N64's kiddy image. Prime 2 was after kiddy-fied Zelda, the Mario Sunshine ad campaign, and Nintendo's very public anti-online stance. The Cube had been written off as the 3rd-place console (although it might've still been 2nd worldwide), and Prime 2 launched in the shadow of Halo 2's multi-trillion dollar ad campaign.
Metroid sells fine. It's never been, and never will be a mega-hit. It could've done better if Nintendo tried harder to help it, but it's doing as well as anyone should've expected.