SPOILERS may be revealed so continue at your own risk!
I have not yet played past the end of WiH Act 2 so I don't know what you have in store for the plot buuuuuuuut I have read Morrigan in Shadow. I really like the idea of Laporte going AWOL and trying to release the Shivans from Capella so they'll decimate the GTVA. This, for me, is the pinnacle of a Freespace sequel. I think BP could stand as Freespace 3 if the plot decides to go this direction. Gotta have more Shivans!
Also, this next idea was slightly inspired by Rogue One. If Laporte did decide to release the Shivans from Capella, she'd have to open a node somehow. An epic hijack mission of the GTVA Knossos portal (from the beginning of AoA) would be suuuuuper cool. Laporte would somehow convince a handful of people to accompany her insane plot, commandeer the station and then transport it to the place where it would reopen the node to Capella. Against-overwhelming-odds missions like this are my personal favorite.
Then there's the obvious issue of the unstoppable Shivans rampaging their way through the Sol system. How would they be stopped for the third time? Maybe the ETAK project is some kind of ace in the hole. They'd have to hunt it down (or its remnants) and it would somehow help them stop the Shivans. I dunno. But I personally believe that this kind of insanely epic ending would wrap things up quite nicely
Just my musings today, carry on...