Of course, you're forgetting about 100 additional VC games, of which several are very rare, you're forgetting the Godfather, Super Paper Mario, Wii Sports, Mortal Kombat Wii, Mario Party 8 (that one's borderline, though), Tiger Woods Golf, and Trauma Center too. Don't forget Excite Truck. If you include ports, remakes, and games on the borderline between great and average, do so for both sides of the argument.
You also left off Sonic Adventure 2: Battle for the Gamecube, which was also a big seller, and a big hit to some. Essentially, I'd say the line-ups are on par with each other when it comes to decent games, while the Wii has several more games in total, it suffers from a lower percentage of great games than the GC had. It boils down to the fact that Wii owners have more variety in titles to choose from, so that one title might not seem like a grade "A" title to almost anyone, but will appeal to a few consumers. If the Wii has the same amount of games that most people like as the GC does, at least in relation to the amount of time on shelves, it has two or three extra "niche" titles for every Cube game at this point, which, all-in-all is similar to the reasons why the PS2 was successful over the GC.
Your concern about Metroid Prime 3 is very valid, though. In my opinion, I think the title will receive great support on either of two factors: Media recognition and/or multiplayer. I think if the media as a whole treats Metroid Prime 3 almost as well as the original Halo was treated, it will do great and sell well, but for this to happen, Nintendo may need to begin advertising campaigns soon. If the game has any decent multiplayer, the internet will chat up about it, and in return, it will be brought into public eye. My criticism is that if the game doesn't reach the public eye, the public probably won't respond well enough to it.
Of course, if they pack in a Wii-remote with it, it will sell well, think Wii-Play.