I remember liking Fusion more than most people at the time it came out, though I didn't disagree with the criticisms about it being too talky or too linear. Maybe I should give it a revisit and see if I still like it that much.
I'll say this, the SA-X setpieces are some of the most tense and frightening moments in the series. It seems like they've been trying to recapture that tension ever since, like with the EMMIs, but failing. The only thing that gets close are encounters with Metroids themselves in 1, Super, and Prime, imho. (Remember in Prime when you found the breached Metroid containment and then the lights went out? Or was it vice-versa? Regardless, I remember that setpiece and hooboy was it a good one for Alien-style Space Terror). I agree that the villain in this being Just Samus makes it all the more terrifying, because it adds a Terminator vibe to the usual Alien one. She's (it's?) a killing machine, and you know exactly how powerful it is, and it is coming for you and will not stop.
Speaking of which, the Alien influence is well-known and obvious, but I think by Fusion it's also kind of worn-out. We already know that Samus becomes an unstoppable killing machine by the end, and the fear of these creeping aliens (metroids) leaping at us from the darkness is somewhat tempered. In the same way that Alien shifted to more action-y vibes with Aliens, it seems the series has done the same, and probably for the same reasons (we know they can be beaten, but can you beat more?) There's kind of two main vibes in the series, where Samus is either the Hunter, or the Hunted. I wonder if there's a way to recapture that original/Super vibe of being the Hunted, of lost and alone, stranded in a place populated by dangerous aliens, rather than being the Hunter (which started as early as Metroid 2), where you're there to kick ass and take names. The EMMIs tried but I think a lot of us would agree that they failed in making Samus the hunted again. Was Fusion the last time we had that Hunted vibe?