I think it is clear that over the years Michael placed more trust in Neri, and used Neri as an advisor more than he used him as just muscle. Neri simply rose up higher in the organization. I dont think it was anything more than Michael deciding Neri had more brains, and I think Rocco was always a little jealouos...much as it might be if two people began employment at the same time and one rose up higher in the organization than the other.