I'm not an expert but as far as I can tell, the best use of sub-species is to put them on planet or moons that are outside of habitable range of the main specie. For example, a low gravity moon that has many nice stuff could have a sub-specie human that can tolerate this lower gravity. This will make it so that ONLY that sub-species live there since regular humans cannot.
Sometimes you get an alien race which requires less oxygen, and this can make it dramatically cheaper to terraform worlds for them. Not only do you need to add less oxygen, but you can also get away with less of the "filler" gases like nitrogen because you only need enough so that the oxygen is less than 30% of the total. I don't know if this can be achieved with human sub-species or not.