One of the telling lines of all this is when he tells Kay that Tom is going to be named consigliere...when he does so he makes it a point to say that Tom is not a Sicilian, and he says it in a disparaging way. He even looks away from Kay when he says it. Implicitly he is saying he doesn't think Tom is the right choice, but instead is getting the job because of Tom's closeness to Vito.
While it's easy to put that interpretation on Michael's comments in light of what came later, I think Michael's demeanor in that scene says otherwise.
While he does add the caveat of Tom not being a Sicilian, to me Michael seems approving of the selection of Tom as
consigliere, and somewhat proud of him as well.
The flashback scene notwithstanding, I think Michael's attitude toward Tom changed as Michael himself changed over the years.
