I think one of the long term goals is to escape the ship.
As such, I think that some of the powers to develop are new masks. Instead of developing natural weapons for this one mask, new masks should be developed to create whole sets of natural weapons. Our originator expressed difficulty in taking physical form, so I suspect a strong connection to physical reality in addition to the ability to control dust will serve us better than taking one path or another.
IOW, we should develop different forms.
Now we don't know much about what we'll want or where we'll go, so I'd recommend concentrating on environments.
Environments we should have masks for:
Void of Space
Air/Gaseous environments.
Water/Liquid environments.
Land/Solid environments.
(Two kinds, ones you walk on and ones you dig through.)
Now we don't know what we should use, but here's my initial suggestions for each one:
Space: Self-contained spaceship. A simple ovoid device with modularity we can take advantage of as we learn more capabilities. Roughly egg-shaped. Should have some kinda sensors, some kinda protection and heat shield, and long range communications devices.
Air: I'd recommend one that's very large, for things like gas giants or wild environments, or combat-heavy environments, and one that's small, for environments which we'll be sharing with other creatures. If possible, something around hummingbird size would work.. I feel that becoming an insect or a swarm of them is a bit too fragile to be safe and may not be able to store enough dust for our actual abilities.
So.. big flier, small bird.
Water: We can get away with one here. Probably something along the line of a dolphin would be ideal. We don't need hands or other manipulators for objects, and a dolphin shape is very effective at moving.
Burrower: Here I think we want a multi-limbed insectoid type with a hard shell and a wide variety of tools, because we will be wanting manipulators even if only to save on effort from transmuting elements in front of us all day.
Walker: Humans are obvious. Here I'd recommend picking one less-distinct form and one heavy form for fighting.. they can both be humans, or one could be non-human. Could also go with a humanoid but nonhuman design, for one or both, but I think one good normal-looking infiltrator would be a good idea, and one good fighty design would be another.
As for what these units need, I think matter manipulation is much more important than simply relying upon dust-related powers forever.. I think it's a mistake to solely rely upon dust, as we may not discover anything new that way, only exploring things that can be overriden or overpowered by the will of others.. if we need to combat someone with a greater will, we need physical objects to defeat that challenge.
So, we should try to develop one physical weapon. I'd recommend a simple fusion-powered laser would be fine, for now, and we should develop some implausably hard material for physical combat, to be our sword or our fangs and claws. Molecular-level mettalurgy should let us make some extremely potent materials like this. Both of these should be usable in our various forms.
One last thing, I think Basil might have the ability to neutralize dust with two cores, by issuing simultaneous contradictory orders. I don't know how to explore this, but it might be a powerful tool for neutralizing other dust-users.