Coming from a Game Informer interview with series producer Yoshio Sakamoto...
“Through the development of Metroid: Samus Returns, I was able to really grasp the possibility and fun of a 2D Metroid. Like when I finished the first game, if there is another opportunity to make another Metroid, that is something that I would love to do. Of course, that really depends on how much people really want to buy a 2D Metroid.”
Source
I'm sure it will depend on the sales of Samus Returns and having a new 2D Metroid would be better then a remake of Fusion next.
“Through the development of Metroid: Samus Returns, I was able to really grasp the possibility and fun of a 2D Metroid. Like when I finished the first game, if there is another opportunity to make another Metroid, that is something that I would love to do. Of course, that really depends on how much people really want to buy a 2D Metroid.”
Source
I'm sure it will depend on the sales of Samus Returns and having a new 2D Metroid would be better then a remake of Fusion next.