I have a lot more thoughts about this game than I do about most Metroidvanias, so that's worth something already.
I find it interesting that the exploration is not what is the best part of the game, but instead it's atmosphere. Rather than feeling like an adventure through an alien planet, this game almost has the atmosphere of a survival horror game. There is an active threat in this area that is thinking and planning as much (if not more) than you are, and it knows this environment better than you do. You're not running around for fun, you're running around to stop the X from taking over/destroying the entire ship. This is way more engaging to me, personally, though I will admit I'm not super into Metroidvanias in general.
Another part I like is how the game constantly keeps you on your toes. Just when you think the game is falling into a rhythm, the elevator stops while you're in it, or you fall into a room with SA-X.
I also like the way that the exploration actively adds to the "going rogue" atmosphere. At the start you're following orders and being pointed to the next spot on the map, but as time goes on you have to start improvising routes, finding spots that aren't marked on the map, cutting through secret passages that get you between sectors without using the elevators, and that's to say nothing of all the times you indirectly go against orders just to go back to old areas and get items.
I do think the game has some flaws, mainly in terms of how much the exploration side of the Metroidvania gets sacrificed. The game feels incredibly linear at times, and there were moments when I wanted to explore and felt that there were arbitrary restrictions in place to keep me on the rails. For every really tense moment, there has to be a bunch of obstacle setting and door sealing to make sure the player goes on the route to actually see it as intended.
It's worth noting that Metroid Prime came out a single day before this game, meaning they were being developed at the same time. Prime also had storytelling, but its was different in that all of it was told through scannable things, such as walls or computers. This is a story that lets the player read it at their leisure, and if they don't want that, they don't have to read it at all. In hindsight, I think this type of storytelling lends itself better to the metroidvania playstyle, but I still admit that Fusion's more linear storytelling did provide for a lot of more memorable moments.

It's fun and all but there's so much backtracking in this game, it's unreal. I'm not just talking about chapter 7. It feels like every chapter has some unnecessary walking to A and B and back to A and maybe even back to B after that, especially if you want badges. People also act like this game has a way better plot than other mario RPGs. It doesn't? The villains aren't characterized at all. This is one of those games that a ton of people say is the best in the world despite not having played it in 10 years. It has soul, but not much substance.