But those came for different Platforms. Prime was for the Gamecube, Fusion for the GBA. Here, both would come for the same platform and would have eaten each other's sales if they released like that.
You seriously think Gamecube owners and GBA owners were such a different audience that the people buying Fusion and Prime were all that different? There was a promotion for people who bought both to be able to play the original Metroid for free and get the Fusion suit in Prime if you linked them. They went on to become two of the best selling in the series, with Prime being the best, and Fusion being the best selling portable title after the Game Boy one. They're the only two Metroid titles released after Super Metroid to outsell it. Nintendo doesn't even have two consoles to release two separate Metroid games on anymore. They sold well despite being released at the same time not because they were on different systems selling to different audiences, but because they both sold to the same hardcore Nintendo and Metroid fans that had both systems, but gave those fans two very different experiences. Why would someone not buy Prime or Fusion just because they'd bought the other? They're different experiences, if you only bought one, it was because you only liked one of the experiences on offer, not because you only had one console. Or do you think Prime, the better selling game on Gamecube, attracted that many more people from its audience that was quarter the size of Fusion's on GBA, which sold over a million less? Why on earth would Metroid fans be less likely to buy both titles if they were on the same system than if they were on different ones? Being on the same system means you only have to buy one system, which makes it much damn easier to keep up with a series. Trust me, I'm a Kingdom Hearts fan.
Also, keep in mind that this could be a port of Samus Returns from the 3DS, or a remake of Super Metroid in the same style, both of which could be done in pretty short development times, enough that they could have been started after the decision to scrap and restart Prime 4 was already made.