I think Clotheshanger has the basic premise. IMO, the whole Vincent-Mary storyline is what really disrupts not only the flow of the film, but the complexity and duplicity of the rest of it.

After seeing the deleted, extended scence between Michael & Gilday, where Michael offers the $$ in exchange for control of Immobiliare, I think the scene belonged at the beginning of the film. FFC screwed up by putting it later in the film as opposed to the beginning. If that scene begins the film and is followed by Michael receiving the honor by the Pope, the storyline has a better flow.