The issue is not simply a matter of "favorites", and neither should be the recommendations.
Prometheus certainly has "atmosphere", and very developed and strong composition. Take the opening to "The Tongue of Fire" or "Wordless Chamber"- incredible layering and drum work that goes far beyond the emphasis on speed found on IX, and to a large degree, Anthems as well. What makes Emperor great is not the blastbeats, its when they are more subtle and let the melody form the intensity.
edit: I do agree that their early work had a raw ferocity that is not found on later works, nor should it. That is what makes Prometheus great- its weathered and very somber.