The way I've seen Sakamoto talk about the Prime Trilogy, I always assumed he saw it in a "yeah it's okay for what it is but it's not the true Metroid that we make" kinda way. Which is a bummer, 'cause I was really looking forward to some Prime stuff (Luminoth, Sylux, CRAZY PIRATE DATA) in Other M.
As for where to take the series after Fusion, there's always the chance that the Galactic Feds made some more Metroids somewhere besides BSL, isn't there? Or, hell, somebody captures Samus within the first hour of gameplay, takes some of her blood, and synthesizes new Metroids from that. This series' science is about as soft as you can get, so there's no shortage of ways to bring the little bastards back as long as Samus is still kicking.