Alright, here's my thinking as it stand right now, tell me what you think.
The Papal States are not going to be conquered by the Romans (or Greeks if you must). That was never my intention. What I think likely will happen, however, is that the Pope will be stripped by the council of his temperal power. After all, the council is 1) anti-pope power, and so would welcome an opportunity to limit the pope's power and 2) pro-reform, and one of the major topics of reform is limit the wealth/power of prelates so that they could more conform to the monastic ideal.
Now that we've established that the Papal States will no longer be the Pope's (and if he fights the council's wishes, the use of mercenaries is not out of the question, its been done, against this very pope, a few short years before), whose will it become? As das pointed out, no one wants a Roman Republic, so that's out of the question. It can't be one of the major powers, because that would probably spark a war. So it has to be some minor branch of some minor noble family somewhere.
Enter the Palaiologos. They would most likely be at their height of popularity in the West right now, after all, they almost single handedly delivered the church union. However, they are militarily weak, needing the West to come save them, so obviously they are no threat to the territories surrounding the Papal States to embark on wars of conquest. Yes, they might be too militarily weak, unable to hold on to the Papal States, but that would play into the councils hands. After all, they may need to appeal to the council for help, which would put them even further in the councils debt. All in all, setting them up perfectly for the role of weak puppets.
So who would be most likely to ascend the Roman throne? Depends on the timing. If the council moves immediately in its steps towards reform/neutering the pope, they would do it immediately, so around 1439. That may make Constantine the most likely candidate. After all, he was just regent of Constantinople, and so needs a nice province to run as a reward. The other option is taking these actions in the next council, in other words 1450. In this case, I am thinking Thomas, or else some really minor relative, (Graitzas Palaiologos would make an interesting choice here). Now Emperor Constantine wants to ship off Demetrios as far as possible, true, but Demetrios also humiliated everyone by throwing a fit over the unification and leaving Italy before the council was over, so he is unacceptable to the council. Thus, Thomas, or an even more interesting choice, Graitzas.