First, I'd like to say that I love the FS2 plot. FS1 had a more epic finale IMO, but overall FS2 was more in depth. But there was always one part that seemed strange to me. After the events of "Straight, No Chaser", the player naturally would be shaken up a bit, with the discovery of a second Sathanas. In the debriefing however, the Vasudan squad leader (do we ever get his name?) says that there are multiple Juggernauts in the nebula. He says this in such a "Oh, by the way..." manner that it doesn't give much weight to the revelation. Also, in "Into the Lion's Den", Snipes refers to the Sathanas that almost hits you as "Sathanas Number 3" instead of number 8 or 13 or something. If he knew about the second Sathanas, shouldn't he also know about the others, even if he and/or command doesn't know the exact number? I think that at some point, the plot was changed and that changing it back would make the whole story that much better.
You have the player and everyone else think that there is only a second Sathanas headed to Capella. That would still initiate the evacuation of the Nebula (and the continuing evacuation of Capella too). Rescuing the Aquitaine in the next mission would still make sense. By the way, in that mission ("Argonautica"), there is an unused debriefing stage applauding you for sighting the (singular) Shivan juggernaut.
When you get to "Into the Lion's Den", the revelation of a THIRD sathanas will be even more shocking, kinda literally. And each new Sathanas sighted will make it even more menacing, making it a very dramatic slow reveal instead of a ho-hum "By the way...". Snipes' comments would make much more sense ("We got to warn the Alliance!"). In the success debriefing, he says that he warned the Alliance that multiple Juggernauts are headed to Capella. That wouldn't make much sense if they already knew that. You could have Xinny and Zero mildly freaking out (why don't they talk in the mission?) to add to the drama. This mission is already pretty epic and I think that a few changes would make it even more epic, along with the entire storyline.
As far as I can see, the only changes needed would be the debrief for "Straight, No Chaser", saying that there is only another Sathanas, and the Command Brief for "Exodus", officially revealing the existence of multiple Juggernauts, since the SOC missions are optional.