I have been with Freespace since the beginning and since my therory hasn't been mentioned, here it comes.
In the ancient's monologes it is mentioned that the destroyers did not come until they went into subspace. The ancients killed lots of civilations, but I believe non of them had access to subspace technologie and that's why they were so easy to kill.
Now the ancients found the shivans and I believe the ancients also attacked the shivans. From the story I would say the ancients won a few victories...but then the shivans came up with a superweapon, aka new technologie that wasn't neccessarily far superior to the ancients, just the ancients had no defends against it.
This superweapon was the Lucifer class destroyer. And here comes why.
Looking at the Lucifer class instead of the other destroyer classes you can easily see that it has a lot of reactors, compared to it's size. It also has this super-shield and the shivan super laser. I beleive the Lucifer is equivalent to a fast attack craft whose sole purpose is attack. Similar to a Los Angeles class submarine. It's a Hunter-Killer, designed to obliterate warships. And that's where the ancients failed, I think they could easily wipe out the shivans fleet, until those Lucifer class warships with the impenetrable shield came to the battlefield. The ancients had no solution to attacking them until it was too late.
Now in contrast the Santhanas class is not a Hunter-Killer. It's big bulky, slow moving, defensless from the back, no permanent shield, only a few reactors... It's more like a mulitpurpose station, who just seems as powerful as the Lucifer because it's soo big.
The point I want to make is, the role of the Lucifer is for a fast paced war, moving swiftly around and destroying well defended and high importance targets, like a submarine so to say, while the Santhanas are like a big station moving around doing several missions than just destruction.
Ok, giving this background here comes my take on the story line. Why do the smaller warships, aka cruisers and destroyers do not have beam weapons in FS1?
I think that the LF were the survivors of the fleet that destroyed the ancients but could not return to shivan controlled space or resupply themselves with energy. The reason for this is that the ancients simply turned off the Gamma Droconis Knossos like GTVA tried to do. Just that it worked for the ancients, they deigned it, maybe they also did something like collapsing the node after turning off the Knossos. That's why the LF could not return. Now from the monologes it is clear that the shivans did not get resources from planets or territories, aka not even the suns, so the LF literally was hanging out in GTVA space for 8000 years without getting new resources or energy, that's why they couldn't use beam weapons.
Now the all important questions, why were the Shivans attacking? Attacking the GTVA, ancients are gone...
Not to get territory, not for the resources, not to get slaves, or power, but for something far more important to them. They were defending themselves and no not before the mighty space fleet but before the side effect of what terrans and vasudans caused.
The shivans live or were born or at least have a close relationship with subspace. I think they are depending on it, might it be for communication, that whole hive thing, or resources, or something like a gravity field, whatever it is the shivans have a close relationship with subspace. And subspace travel is disrupting this. Basically subspace travel is destroying something important to them and they want to stop it. I think this is very clear in the game. The ancients could destroy civilisations, they could cause whatever mahem they did, without any attention from the shivans, but as soon as they constructed the knossos and travelled through subspace the war with the shivans started. Why? Because subspace travel causes problems, either to the universe or to the shivans directly.
I hate to give the following analogy, but think about StarTrek and the concept that all ships are only allowed to go a certain Warp speed or they cause, a rift in space, aka a black hole. This could be the whole reason for the shivans attacking. They let your civilation evolve in peace until you reach the technological level to travel subspace. Not to protect you, but because you do not cause damage until you reach this technological state. Then they come and wipe you out. In FS1 they went straight for Vasuda Prime and then stright for Sol, why? Not because there the most people were or because of the political center, but because from their the most subspace travels came. Those planets were the capitals, they were the powerbases, so those two systems caused the most damage to the subspace because there were so many ships.
Probably this is also the reason why the shivans started the first Great War. Because the terrans and vasudans travelled so much thourgh the jumpnodes in the T-V that the LF which lay more or less dorment without much energy for 8000 years, woke up and had to stop them.
Now in FS2 the shivans were different fromt he shivans in FS1 because the there was a 8000 year gab between the two forces. The important thing to remember is that the shivans behaved differently. In the first war they had to stop those terrans and vasudans from continuing to use jumpnodes, so since you got limited resources, you have to anniliate asap. In the second war, the shivans were first under attack, the GTVA went into the nebula, destroyed the gas miners, aka shivan civilians, and even went into their controlled space. So the shivans were under attack. Remember those communication stations, they could for all we know also have been civilian places, they were not even well defended. So detryoing those civilian installation and killing a number of shivans in their space showed them that this enemy is for real and powerful. Since they suffered losses, they prepared for a major campaign, and that's where those 80 Santhanas came into place. I think the 80 Santhanas were not send in for the purpose of whipping out the GTVA but to create a command outpost. Since the shivans get their energy and resources from a nebula, but not normal systems it was clear that the first step was to create a new nebula, and capella was the perfect location, with 3 jumpnodes into all directions. So I think the shivans were merely destroying capella to create a huge base to start attacks into the GTVA territory with more advanced ships aka Hunter-Killer ships like the Lucifer class ships with permanent shields.
Also I believe the shivans are very slow in advancing technology wise. They do not addept or change, but have their technology, and that's about it. So I do not think that the shivans in FS2 knew how small the GTVA really was but that they expected a major fight, like against the ancients, to finally stop them from using the jumpnodes.
Last point about the destruction of the Santhanas class ships during the supernova in capella. Who says those ships were not empty, remote controlled. The just activated the jump field and then evacuated the ships that stayed behind. Sacrificing a few empty ships for generating a nebula which brings them about unlimited resources for this major conflict sounds logical to me.
Ok, that's my take on it. I hope this opens the door for new discusions... ; )
ICE