I have a slightly different take on the change in Pacino. I did not see either of the first two "Godfather" films until 2000-01. So the Pacino I was used to was the gravelly voiced one from "Heat," "Sea of Love," "Donnie Brasco," and "The Insider."
For me, the first couple of times I saw the original "Godfather," I really had a hard time believing it was the same Al Pacino. More than anything, I think the smoking really took a toll on Al's voice. Obviously, we all change in physical appearance over time. But the vocal change was so pronounced.
The most disturbing aspect about Al for me in "GF III" was that ridiculous haircut. I cannot see Michael Corleone ever wearing his hear like that. A spiked haircut does not befit the Godfather of the most famous fictional crime families.