I suppose Savoy and Venice would both be indepedant in this scernario?
Which scenario? The Cesare Borgia one?
Quite a lot of things will be independant (or at least not controlled by the Papacy) for quite some time, no matter how well things turn out for Cesare.
Historically he controlled the Romagna and was in a position to invade Tuscany in 1503, when Alexander VI died, Cesare fell ill and was suckered by Cardinal della Rovere into supporting his election as Pope. Ironically, after getting rid of Cesare, Pope Julius II tried to follow through with the Borgia plan of turning the Papal State into a major secular power, but ultimately failed because he lacked the military muscle to lead his own alliances, and his various Leagues succeeded only in replacing one occupying power with another, with Italy weakening with every new war.
Suppose Alexander VI lives another couple of years. Cesare marches on Tuscany, forces Siena into his alliance and takes Florence. When Alexander dies, he takes Machiavelli's advice and alles with Spain (which has just pushed the French out of Naples). A compliant Spaniard is made Pope, with Cesare as Captain-General and de facto Prime Minister. Assuming this all stands up, in a few years' time he's in a position to move against Venice, and with the Spanish alliance and the wealth of Florence he has no need to bring in the French (as Julius II was forced to, only to watch them reap the spoils). Venice is defeated (as per OTL), and the Papal State takes control of (or at least hegemony over) Mantua, Ferrara and the former Venetian territories around Padua. The price of Spanish support will likely be to help remove the French from Lombardy (which Cesare wants to do anyway). The French are defeated (Cesare and Gonzalo de Cordoba are a scary combination), Milan becomes a Hapsburg possesion and the Papal State takes Modena. When the dust settles, the Spanish have Naples and Milan, Venice retains the Veneto and the Papal State has pretty much everything in between (though its control of the northern duchies is likely to be fairly loose).
That's about as much as Cesare can hope for, even if dad is pulling for him in Heaven. But the Papacy is now the pre-eminent Italian state and a genuine player, rather than a pawn, on the European stage. A later ruler could ally with France to break the Spanish hold on southern Italy, then swap back to the Hapsburgs against the French and so on, gaining every cycle. Venice, Genoa and Savoy will be the last stages in the process, which could well take centuries.