Lots of incorrect assumptions here, let's see if we can correct a few.
In the Great War beam cannons were new to the Shivans, but someone had used them on the Ancients 8,000 years ago. (only the lucifer had beams in the great war, but 34 years later every Shivan warship had something).
Who says they were new? It's just as possible that the Shivans simply sent a small fleet of old ships because they didn't think they'd need anything else. They'd be almost right too. The Lucifer came within 3-4 minutes completing its task.
The lucifer fleet was xenocidal, but the Juggernaut fleet is not and even tried to minmize GTVA casualties. (A single sathanas showing up at the Capella/Gamma drax node whould have destroyed all convoys and still been alble to return to the star in time to escape)
Not punching someone in the face beating other people up doesn't count as an attempt to not assault them. It's just as possible you were busy elsewhere.
Whatever the Shivan's goal was in FS2 there's no reason to assume that it wasn't simply an updated goal for the exact same faction.
The icini in the nebula. Why did the Shivans kill almost all of the crew but extract Bosch and key oficers? Did the Shivans just want Bosch for somekind of an experiment, or did Bosch tell the shivans to kill everyon else?
That's the million dollar question.
Shivans were created by some other race, (they have no reproductive organs)
Huge assumption. Where is the reproductive organ on a slug? A female hyena? A worker ant? Can you point those out in only a few seconds of video?
And even if you were right who is to say that the Shivans themselves haven't engineered reproduction out of themselves. Humanity is on the cusp of being able to do that sort of thing right now. If we really wanted to we could probably genetically engineer out the genitals and go to a cloning based reproductive method in a few decades (or centuries at most). Hell we could probably get rid of the male ones in a decade.
And actually it does say the Shivan don't reproduce in a command briefing.
I don't think it does. Certainly not in the FS2 techroom entry if that's what you're on about.
During the Capella incursion, the Shivans seemed to be fighting for their lives.
Eh? 1/10th of the Sathanas fleet could have taken out the GTVA. Why do you believe they were fighting for their lives?
The second nebula knossos and the one beyond it in that next system (into the lion's den). If the Ancients discovered who ever destroyed them in the nebula they wouldn't have the ability to build those remaining two, but if Shivans or who ever was able to get into the nebula why copy Ancient
tech and build them at all? In years past, was the nebula the "destroyers" home world and the Ancients let them out?
Who says that the Ancients discovered their destroyers in the Nebula? That's an enormous assumption which isn't backed up by anything ever said in the game and in fact is directly contradicted by the existence of the other Knossos portals.
Far more likely is that they discovered them somewhere beyond the binary system and retreated back beyond the 1st Knossos as part of their retreat.