Perhaps Michael wasn't thinking that he was going to be a Don yet because Sonny was still alive, but he had to know that after shooting a police captain and fleeing to Sicily, there was no way he was going back to his old life. He was going to be involved in the family business in some capacity, not go on to be a history professor.
As for the Kay's miscarriage, I think he was more upset about the loss of the son, not for Kay. If you remember, when Tom first told him the news, he never once asked after Kay. His only concern was for the baby that was lost.
And regarding the talk with his mother (and I agree that it was one of the most beautiful scenes in the film), I think that Mama misunderstood. He was NOT talking about the miscarriage. He had just found out about Fredo, Connie obviously hated him, and he did feel estranged from his wife. Therefore, he felt that he was "losing" his family. If you recall, Mama says, "You're thinking about the baby that you lost," but I don't think he does.
As for his proposal to Kay, I think that it's rather cold. I didn't feel any great passion coming from him. There was no sense of "You're the love of my life, please come back." It felt more like a business proposition than a proposal. He never even looked for her until he was back over a year.
I agree that in GF3, he wanted some peace with her, but I think that's for his own sense of redemption. I do believe that he regretted his treatment of her, that perhaps he had misled her when he proposed. Of course he loved her on some level. He had built a life with her, she was the mother of the children that he adored, but, again, I never sensed grand passion.