Pretty much everything anyone can think of has already been discussed. I'm just curious as to the most popular and legitimate theory out there.
I'm not so sure of Shivan intentions as to have a definite theory to explain the whole FS2 storyline. I am pretty sure of certain of the Shivan's motives. They're trying to cut off the Terrans and Vasudans, if not necesarily kill them. As mentioned in the FS1 ending, the Shivans exist to protect weaker races from being taken over, and isolating the GTVA by forcing it to destroy the nodes to Sol and Capella seems like something the Shivans would do.
The destruction of the Lucifer stopped the first Shivan invasion, but at the same time the Terrans lost contact with the center of their empire, and the Vasudan homeworld had already been blasted. They'd forced the Terrans/Vasudans to cripple themselves. One of those "Shivans work in mysterious" ways things. I suspect that if the Lucifer had made it through then the Shivans would have collapsed the node anyway. Capella was also an attempt to cut off the GTVA. By blasting the two Capella nodes, the GTVA was sealing itself off from the Knossos network in Gamma Draconis. The Shivans didn't mind; their work was done, the GTVA had shut itself off from expansion, and when Capella was about to be sealed off they blew the star. A few Sathanases stayed behind as garrison.
The FS2 tech description of the Shivans tries to make it clear that the Shivans were constructed by someone else. I won't repeat it word-for-word here, but take a few seconds to read it and you'll see what I'm talking about. It's like Petrarch's out-of-the-blue theory that the Shivans blew up Capella to make their way home: a storyline freebie. Anyway, people are pretty critical of the "Shivans are just taking point for a bigger, badder creator species", but I wouldn't be surprised if Volition really was planning to take the easy way out and turn FS3 into a big final battle between the GTVA and the Shivan's creators. In terms of storyline, FS1 and FS2 weren't all that creative in the first place, unless you compare them to rest of the cliched space shooter genre.
The Shivans couldn't or didn't want to handle the GTVA for whatever reason, so they sealed it off, and left to call in the big guns for Freespace: Episode Three. I mean, if the Shivans are really happy, peaceful people just trying to guard their subspace turf, who's going to be the enemy in FS3 after the Shivan's conversation with Bosch? Petrarch gives us the impression that the Shivans have made their peace with us and left for their homeworld, so who are we gonna fight now?
I know this post is too long for most of you, but one more thing. Volition probably doesn't intend it, but it's very likely that the Shivans may have evolved in the nebula. Scientists have talked about the possibility of hydrogen-based life on Saturn and Jupiter, so why not in the nebula? Plenty of different gases and environmental conditions. Few people realize how huge nebulas are- typically 30+ lightyears "wide" in at least one direction. The odds of life originating in a nebula may actually be much higher than life origination on a planet, simply because of the massive area that could potentially create life. All your basic elements- oxygen, carbon, hydrogen- are there, and the massive size makes it likely that there will be at least some areas with the right gas mixtures and temperature for life to evolve. If you absolutely insist that life needs a solid surface to start from, there are plenty of space rocks floating around. So, not saying that this is a serious theory, but The Nebula(TM) could be the Shivan's "homeworld", and the Capella nebula a second home for them.
So, what's your theory?