The clones could be as human or non-human as the players intend, with the knowledge that the ones which have been enhanced would be the ones with the most amount of power and the more complex missions. Obviously, the clones would be trying to distance themselves from their flawed forefathers and the more they perfect the science of replicating themselves, the more they would try to make themselves superior. Yet with every attempt to achieve perfection, shifts could happen that would make the clones unstable in other areas.
That's a fantastic idea! Hiding in plain sight would make sense and allow the resistance to contact each other wherever they are - and whenever. The clones could be there trying to break the code, for example.