I doubt the end result would have been any different with Duvall in the film. You would still have the large time gap, the modern age story, the convoluted plot, and Sofia Coppola as Mary.

Now with Duvall AND Ryder in the film, then we are getting somewhere.

And I would have hated to see Hagen assassinated. He should have been there on the steps with Mike at the end. I doubt there would have been a power struggle between Neri, etc... it was barely there in Part II and Mike in Part III was already a changed person, filled with regret and probably would have clinged to Tom as the last brother he had.

EDIT: I actually think having Hagen slowly die of cancer would have worked. Have him on his deathbed could have resulted in some awesome flashbacks between Mike and Tom. Couple the loss of Hangen with the death of Mary would have been a far more complex one two punch for Mike to deal with.

Duvall in Part III would have been great just to see him as Tom again.