The nuance of the Enclave doesn't come from the game having characters rationalizing their belief system like they did with the mutant Unity, but through humanizing the people in the Enclave who one would argue were "just doing their jobs". Navarro has a lot of such cases. The game went to lengths to paint Cookie, the Navarro scientists, the vertibird guard, Dr. Curling and several others as surprisingly human folks one might argue were just doing the job assigned to them with no thought to why. Curling being unique in that he did know. He's the closest thing Fallout 2 has to a "Master" moment. But unlike in the Master's case, Curling comes across as brainwashed and can be talked down on moral grounds. The other major oil rig characters were a jaded, spiteful politician and a big thug you can't talk to.
I'm fine with not portraying the Enclave ideology as redeemable(Fallout 2 never did), but to paint ever member of the Enclave as a mustache twirling hive mind with no individuality will always be a downgrade of Fallout 2's portrayal. If you can't expand on that human element the way NV did, don't use the Enclave.