I will say this. In Freespace 1, the Shivans were attacking the GTVA. This we can tell from the end of Freespace 1 (Assuming Alpha 1 knows what the **** he's saying, though since he probably saw the Ancient's cutscenes because he mentions them, I would say he does) In FS2, the Shivans seem much less aggressive than the Lucifer fleet was. (After all, if the Shivans really wanted to, they could have attempted a breakout from the Knossos at any time.) But they didn't. Why not? The Lucifer was destroyed by a last ditch act of desperation on the part of the GTA. Had the mission failed, the GTVA would have been destroyed easily. From this, this is my belief.
1. Regardless of whether or not the Lucifer fleet was seperated from the main Shivan force, the Lucifer fleet's goal was the annihilation of the GTVA.
2. The Sathanas fleet did not attempt to destroy the GTVA, and was only attempting to create a buffer, or the GTVA had really advanced so much that the Shivans simply could not make headway.