Well, FS2 didn't sell well is probably due to the following

-Frankly, I think the problems with the FS series is a sort of lack of involvement with the protagonist (I mean, look, you fly around inside a damn plane regardless of rank on every mission!)
-There are no side characters to keep you entertained (See Ace Combat 5).
-You don't make any decisions in regards of mission objectives (Save for fragging your allies or intentionally warping out at the wrong time).
-The story is quite depressing, but thats only how I feel due to witnessing the massacre at the last mission of the official campagin and the intro animation of the Great War.

-No one ever knows what the protagonist thinking, save for your own interpretation.
If anyone wants to write a storyline for FS3 (say [V], if they're still interested).
They would probably have to explain all the omg-wtf-is-this mysteries involving the first and the second one.
That would include-
Shivans -
*Where, why, and when did they started obliterating everything they see!
*Ross 128
*Capella incident
Terran -
*Whatever happened to Earth/Sol System. Hubble tells us there is now more to the Sol system now than we know then.
*Bosch's involvement of the NTF; the remanents of the NTF.
*Jump nodes! Will they finally go back to earth after spending a few more years building a knossos portal? Or will the Shivans finish one before them and invade from Capella?
Vasudan -
*Them hammer of lights... They're still out there and the destroyers have nearly obliterated the GTVA again (advocate again for the destroyers).
*The relationship between them and the Terrans...
What I think is the most likely scenario in FS3?
-After Capella. The warm-up of the protagonist (You) in rooting out more HoL and NTF leftovers (god knows how many more converts there will be after Capella, knowing the Shivans will come again).
-After all that stuff, you fly around to A) a small skirmish with the shivans B) flying first into Sol.
-Them GTVA goes back and find the Sol system in Ruins or in a state of war. As the first FS indicated, them shivans would have returned to Sol in a few years after the Lucifer.
-Terrans of Sol unites GTVA, they push the Shivans out of Sol before a second Capella occurs.
-Shivan comes back and bite'em in the behind with some super weapon (again).
-You (the protagonist) would fly a series of suicidal missions ranked as an admiral then along with your petty escorts in an attempt to save humanity once more.
-Assuming this is a trilogy, the alliance discovers a weakness or develops a supber-uber weapon to counter the shivans and end the conflict decisively, with the help of the protagonist (you).
that should sum up everything!