Those are really, really upsetting numbers for the Metroid franchise.
Why? Because MP1 sold 2.78 million, probably on the back of reviews claiming it was one of the greatest games of all time. That critical reception would be echoed by the fans - almost everyone agrees it's a masterpiece. You'd expect the next game to do gangbusters having established a bar of quality like that. But instead they lost 1.68 million of the MP1 buyers.
But that's because the Cube was dead / dying, you say. So how do you explain MP3 only selling 1.41 on a system that was moving faster than free money, and had a good motion gimmick to recommend it to casuals? The only answer I can see there is that despite making incredible games and an initial splash, the market simply rejected the Metroid Prime formula. People don't want it. As these are 3 of my favourite games of all time, that is seriously upsetting to me.
It also explains why Nintendo took a hard left turn with Other M. The only consolation is that that shit-fest was properly rejected and didn't reach a million. (I would've cried if I'd seen it on that list.) But if Metroid Prime doesn't work in the market, and Nintendo's best idea fell flat on it's face critically and in terms of sales, then it's very hard to know what the future of the franchise could be.
I see them trying a 'New Super Metroid' type 2D deal. If that doesn't crack 1 million on the 3DS then you couldn't begrudge them shutting it down indefinitely. It doesn't help that Metroid games are probably right behind Zelda as the most expensive games Nintendo makes.
The only good argument for making a new 3D Metroid is if you do it at launch in order to get the hardcore on board and evangelising your system. Because it's the type of game that would make far more noise on the internet than actual sales. That's the best value it would have to Nintendo - giving 'gamer cred' (sorry, I really am) to a newly launched system. Sounds stupid but you want the hardcore gamers both in the media and on message boards on your side early, you want to make a splash at E3 and elsewhere and Metroid is the type of title that will do it. Outside of that, it just doesn't seem to make sense.