Michael lacked his father's warmth. He lacked the ability to inspire love as his father did. I believe the loyalty he got, at least as portrayed in the movie, was inspired more by fear and/or admiration for his cunning, than by love.

As for his uneasiness, he operated under his father's wing for many years. No matter how good his training, he would be a bit insecure to be on his own for the first time. Especially if he had counted on the friendship, and perhaps mentorship, of Clemenza and Tessio, and now Tessio was gone.