I think they tried to throw too many plot threads in there, which made it difficult to suitably resolve any of them.

IMO, the Vatican/Immobilare plot line should have been dramatically reduced in scope and the ascension of Vincent in the family structure should have been more fully explored.

Only Puzo and FFC would know this for sure, but I believe the loss of Robert Duvall and the resultant writing-out of the character of Tom Hagen drastically changed the overall direction of the script.

Clearly, toward the end of GF II, the continuing loyalty of Hagen is an issue. The entire scene at the Nevada house, where Michael puts Hagen on the spot about the job offer from the competing hotels, Hagen's "Why do you hurt me, Michael," and the conversation in Italian ("So, are you staying?" "Yes, I'm staying") very clearly set up the idea that Hagen's loyalty, in the end, may NOT be absolute.

Immediately following those scenes we have Hagen visiting Pentangeli (aka Clemenza) in jail and "explaining" to him the suicide option for long-trusted members who betray the family.

And then, we have Michael's final disposition of the Fredo problem, which shows that Michael's final loyalty is to himself - he would get rid of ANYBODY who he perceives as a threat.

All of this IMO was intended to set up the questions in GF III, whether Hagen's loyalty was absolute, and if not, what Michael would do about it.

Had Duvall been in the GF III cast, my guess is the movie would have centered almost completely on the internal family politics, and external stuff like the Vatican/Immobilare plot line would have been greatly reduced.