They were working on a DS title called Metroid Dread, and it takes place after the events of fusion. See, even if all the metroids are killed off (I wouldn't be surprised that they are not) Samus is now part metroid, filling the title criteria.
Seeing as Metroid was Gunpei Yokoi's mind-child, I wouldn't blame Nintendo for wanting to retire the game in some sense. On the other hand, KSSU hadn't once credited Sakurai, so who knows where their priorities lie.