Subnautica's art direction does give me Metroid Prime vibes.

That's what a lot of the upgrades boil down to, yeah. Air tanks increase endurance, fins and seaglide increase movement speed, rebreather eliminates an endurance draining effect at depth, seabases and submarines allow you to start your dive from greater than zero depth. Pretty much all of that boils down to "dives to this depth are now practicable."

Other than that, the knife allows you to harvest plate coral for making computer chips, kelp for making fabric, and seeds for plants. The scanner is required to obtain the blueprints for several other required buildables. The mobile vehicle bay is required to build the Cyclops. The Cyclops is required to make the shield module. A radiation suit...I think speedrunners don't use it and just tank the damage with medkits, but I consider it a requirement.

There is one straight-up key you have to craft; there are several others for required or optional doors but you only have to craft one to complete the game and two to unlock all doors.

There's a tool that is like Half-Life 2's gravity gun, which can be used to move heavy obstacles out of paths, but it's never outright required for anything. I usually don't bother with it.

The laser cutter is required, You have to cut through one of two doors in the Aurora to gain access to the Captain's Cabin.