Cesare's position was too much based on support from Rome and after his father died, he had to focus on having at least a non-hostile pontiff there, in order to be able to deal with the unavoidable disorder in Romagna.
At this point, leaving Romagna even once dealth with and assuming it doesn't revolt while he goes away, and assuming a longer-living Pius III...
Eventually, his political agresivness would owe him a lot of issues : he faced a general hostility, including within his own troops, but critically in Roma(as neutral between Borgia and Della Rovere Pius III may have been, plundering pontifical finances to conquer Tuscany for Cesare's own benefit was definitely not a good thing on his favor).
And going against Sienna and Pisa, as he wanted, was certain to raise Valois against him, meaning his last ally (or, rather, the closest thing Cesare had from an ally at this point) : Louis XII didn't want Cesare chasing again Pandolfo Petrucci out of his city when he just re-instated him after Cesare's successful ousting of the dictator.
Taking on the newly re-established Republic of Pisa wouldn't be a good idea either on this regard, but it would be more due entering in a real wasp nest : Firenze, Lucca, Roma, France, etc. were all interested on this point, less for strategic importance (altough it counted), but rather for political matters as it was the hotpoint for local states.
Without real support, I doubt Cesare Borgia would have the ressources then to deal with it without political harm and without guarantee managing to establish his domination.