Phantasy Star 5 would probably still take place in the Algo system but perhaps some more locations should be added, perhaps neighboring star systems?
It is a given that the storyline would be very different from the previous three/four games.
Lets take in account that the writers would also be following how other JRPG franchises have been developing campaign wise, rather than repeating the scenario of Phantasy Star 2 (a seemingly Utopian world that hides dark secrets) or Phantasy Star 4 (a world struggling to recover is suffering various setbacks while an ancient evil is about to achieve its goal, the result of culmination of planning for thousands of years), the set up should be some thing new and different, something the previous four (five if we take Adventure into account?) did do every time.
Perhaps the plot should involve the Great Light, showing what its nature is like and deconstructing the trope that light equals good. (in my take the Great Light, thought different from the Profound Darkness would be immoral and unsympathetic in its own way)