I think Battuta probably has hit most of the major notes that V would most likely have gone with: Civil war with Earth, return of the Ancients, Shivans return, head to Shivantown through the Capella system for a final showdown.
But we don't have to predict FS3 here, we have to pitch it. So let's try a different approach. This story would pick up around two decades after FS2, when the GTVA have made contact with two other spacefaring species:
The GTVA are engaged with anti-expansionist (effectively anti-alien) rebels, when one of their new allies reports an encounter with a massive, powerful Shivan fleet (multiple Lucifers, Saths etc.)
The GTVA tries to stop the Shivans, but are outgunned, and the hostile fleet makes a beeline for DS, where the GTVA are building a Knossos portal to Earth.
The GTVA reveal that they have made radio-wave communication with Earth over the years and told them of the continuing and evolving Shivan threat, and believes that Earth, with its decades of studying the Lucifer wreckage and its massive economy and population, has the military prowess to defeat this Shivan invasion, if the GTVA can keep the Shivans away from the knossos long enough to open the gate.
After a massive battle to hold the portal, GTVA scientists manage to stabilize the node and the player jumps through, rallies the forces of Earth (who have been waiting for years following the radio communications) and returns with a fleet at good back to destroy the Shivans in DS and drive them out of GTVA space.
Jump forwards in time eighteen months, and Earth has retaken control over the Terran race, dissolving the formal GTVA by withdrawing from BETAC, imposing militaristic rule and anti-alien laws in line with the rebels the GTVA were fighting at the start of the game - will you, the player stand for this and assist Earth in return for security from the Shivans, or join the resistance and fight for the more egalitarian society you knew?
I know that it incorporates some of the elements of Inferno, BP, and probably some other mods as well, but I think it could be done pretty well, myself, and it keeps the Shivans at a realistic level (I never bought in to BPs whole "Cosmic superentities" thing - I see the future of the Shivans and the GTVA more like the future of earthquakes for people who live in active fault zones: They're an omnipresent threat that could strike at any time and do enormous amounts of damage, but if you're clever and lucky, you can survive these his, just hoping that the big one, when it comes, will be long after you're dead. In this scenario, this Shivan invasion is bad, but its not the big one. Not yet.