I have the same issues with prequels because you are somewhat limited. You can't make a huge impact that would contradict the things presented in the future, and that is exactly what happens for the most of the time. Prequels are so bad seem that many people praise Star Wars III not because it is great at its own, but because it provides a convincing liking to the early Star Wars movies, that were set in the future.
As for a sequel, well, there is always room. They would have to deal with the fact that Profound Darkness has been killed in PSIV, so, in theory, Dark Force should not exist anymore. I don't see as a good alternative for them to return to Algo, because when they left, they didn't know what has happened to their former solar system. They don't know if it was completely destroyed, like Palma.
Of the endings, the ending where they end up in Earth just closes the story with PSII, creating an unending cycle. All the other endings could provide a sequence, but there I'd like that it would be a Dark Force-free future, since its source should have been destroyed in PSIV. What they could assume is that the Great Light - Profound Darkness thing only worked for Algo and that evil could exist somewhere else without the influence of Dark Force. Being so, there are many possibilities: colonizing an uninhabited planet and inner struggles that could appear (as it is in our world), colonizing an inhabited planet and a further war between Algolians and the rest, both Alisa III and Neo-Palm colonizing different planets and a future war among them or even each ship colonizing different planets and two threads of story following from there. They just had to come up with a convincing plot and they would have a good chance of keep on the PS series. I think also that PSIII future offers more convincing opportunities than PSIV future.