"Where did the inspiration for the almost-but-not-quite human Manikin characters come from?"
In order to effectively represent the war between Reasons that's going on in the Vortex World, we decided on the existence of the Manikins. In a country or in a company, power is a measure of numbers. A populous country can collect more taxes, and a company with a larger work force can undertake many projects. We wanted the Manikins to represent this overwhelming power in the Vortex World, to fuel the groups in power in the Vortex and to be able to press for the birth of a new world. The Manikins are born from the earth of the Vortex, so could be seen as something like the Vortex's cells. What form the organization of those cells would take should change with what Reason they're fighting for.
Since the Manikins are, as it were, the Vortex itself, they don't have individual goals, but as the Vortex is searching for its Reason, as parts of the Vortex, the Manakins must look for that Reason as well. Since they don't have personal goals, but serve as a strong basis for judgement, and since there are so many of them, they make for an effective intensification of the great war.
As for the Manakins' distinctive conceptualized motif, that comes from us, the way humans think and act. This is a bit vague, but they are based off of the people who're lost to the force of numbers.
For instance, someone who doesn't see movies much but goes to see one that's topical or popular, or buys a CD because it's sold a million copies, without any personal judgement on the matter, and feels that this is the way everyone should be, would be a good candidate for this kind of judgement. It's hard to tell exactly where to draw the line and it is likely that the vast majority of people have this inclination, but there are people among them who almost entirely base their judgement on this strength of numbers. The Manikins are a metaphor for these kinds of people. When you're thinking about buying a game not because it's a game you'll actually like, but because it is advertised a lot and everyone else is playing it, that is acting like a Manikin.
(Source: Q&A Section, Shin Megami Tensei: Nocturne Strategy Guide)