This annoyed me also.

If the Avatar universe has physics like ours, which it looks like it does from the way things move etc..

The protoplanetry disk that the planet formed from, must have had the unobtanium, since it is so evenly spread around the later formed planet.

Yes, there are higher concentrations in various places, which could have come from impact events in the past; if this is the case the impactors are likely from the local asteroid belt or equivalent.

The unobtanium must be available, in a much easier to extract form, in asteroids in the soloar system or the moons of Pandora.

Either way, a mineral is a terrible maguffin for a space faring civilization.

In the second movie, the whale brain juice is a much better maguffin, but still kinda stupid for a technologically advanced species.

Assume that to get interstellar travel, with the suspended animation and brain beaming tech we are shown, humans are a good 200 years ahead of where we are now....given that they can also make fully functional alien bodies from scratch, that can breed and pass on genetic material to what look like viable offspring. The level of synthetic biology expertise must be insane, and they can't make this brain juice....it is just stupid.