The way I see it is that Michael wanted to churn his (illegally obtained) funds into Immobiliare (a legitimate business on the face of it), in order to finally 'go straight' and leave the illegitimate world behind him. Remember how the archbishop tells him how the deal with Immobiliare will wash Michael and his entire family's history clean away.

The deal would also make Michael extremely wealthy, amongst the richest in the world. This would obviously pose a great threat from his enemies point of view.

The Vatican own shares in Immobiliare, Michael makes the deal to buy them, pay off the church's debts, and this is agreed at the initial vote which I think is in New York, and the deal is subject to ratification in Rome.

What Michael may or may not know is that Luccesi is running things behind the scenes, he doesn't want Michael to take control of Immobiliare because of the threat it poses to his own position, and therefore Kleinzig (the swiss banker) who is in Luccesi's pocket, is instucted to veto the deal at the ratification stage. Michael and his lawyer believed the ratificatin meeting to be only a formality, so were understandably furious when the deal fell through.

What I don't quite get is that if the Archbishop was working for Luccesi, why would he agree to the deal with Michael in the first place??