Obviously the scope of the Shivans, the GTVA, and the Freespace universe has been given a tremendous degree of depth in the BP universe.
We already know from Morgan in the Shadows (although that is not an exact parallel), and some answers here about Feds fighting Shivans, that the Feds and Teves aren't going to murder each other back to the stone age. At SOME point, the greater battle against the Shivans/Darkness is going to return.
It's already been stated that the Shivans are in essence, a force of nature or a galactic immune system, one essentially impossible to destroy. Not counting the ongoing existential threats to the universe.
That being said, this is also a space game where the player character has to make some kind of impact with all the shooty and exploding space ship bits (I don't expect the BP story to be "all for nothing," you guys are better writers that that).
A lot of prefacing to ask the following: can we expect a CONCLUSION to the Shivan threat in a Third Incursion? Whether humanity's reunification to face a common enemy convinces the powers that be there is still virtue and valor left in our races, or decide simply going out guns blazing, a lot of fans, myself included, do view BP as sort of the epilogue in spirit to the Freespace story. That's not to say you guys don't have the right to tell your own story, but rather, the fans would like a satisfactory moment of catharsis against a race of cosmic destroyers. It's a fight we never got to finish due to the end of Volition.