I mean most writers have praised Cesare's governing of the Romagna so its not like he was a bad ruler.
Machievelli's rule 1 : being a "praised" ruler never solved anything by itself.
More seriously, Cesar Borgia's dominions depended heavily from the legitimacy his father gave him. After his death, everything crumbled, depsite Cesar being undoubtly skilled.
Could Cesar having kept control of papacy? Really hardly : he made mainy ennemies within the traditional roman elite and could only influence the vote by staying in Rome itself.
Doing that, however, would be the signal of rebellion in his italian holdings : it's what happened OTL while he was in Rome during the election of Pius II, and there's no reason that it wouldn't happen ITTL.
Now, WI Pius II doesn't die so soon? Well, maybe you'll have sort of concilation with Cesar keeping his Romagna's holdings in the name of the pope (as he did during his father's reign) but being more far from strict roman policies.
Personally, I don't think it would last : except a french support, Cesar was too isolated and his political agressivness would lead him sooner or later to fight with friends of roman elite and even papacy.