An On-Topic Reply (imagine that)" I'm just going to comment on a few select blocks of text in the order which they appeared:
The Shivans appear to lack the expertise needed to shield a capital-class vessel, with one notable exception: the heavily-armed superdestroyer Lucifer was protected by an impenetrable energy shield, likely energized by the ship's five reactors. Allied craft were never able to penetrate the shield directly, and were forced to circumvent the mechanism entirely by ambushing the Lucifer during subspace transit, a time during which its shields would not function.
The Lucifer-class vessel destroyed at the close of the Great War was the only known craft of its type to exist in the entire Shivan armada. After 32 years, the design may now be obsolete, or the superdestroyers themselves might only be manufactured in minimal numbers. We have no way of confirming either hypothesis.
The Lucifer Super Destroyer (or something like it) has been inservice for thousands of years, we know this because the Ancients fought against a shielded warship and lost. I think its unreasonable to assume that
1. the Lucifer is a unique vessel
2. that the Lucifer was the same ship to fight the ancients
Just because there aren't any Lucifers in FS2 doesn't mean they're aren't more around.
d. Is it possible that the Shivans captured Bosch in order to interrogate him?
Unlikely. The Shivans have never previously been interested in talking to either Terrans or Vasudans, and have never taken prisoners (with the exception of Bosch and his command crew). We are granted very few glimpses of Shivan/Terran personal interaction: once in the "Hall Fight" cutscene, and again with the apperance of the Lucifer at Tombaugh Station (described in the Freespace Reference Bible). We may or may not wish to include the boarding of the Iceni as a third example. In each case, contact has been extremely violent, with no intent to discuss any sort of terms, or indeed, to ask questions of any sort.
I think this statement is somewhat contradictory. You say that the Shivans have never been interested in taking prisoners and yet at the same time say that Shivans won't interrogate (ie talk to) Bosch. Well if they're not going to talk to him, what the heck was the point of taking him alive?? From the fact that Bosch was taken we can assume three things:
1. There is no prior evidence of Shivans boarding Terran or Vasudan vessels; the fact that they've never used ground troops suggests that such an occurance is extraordinary.
2. The shivans knew who Bosch was ; in a ship with thousands of crew members, only Bosch and his officers were not killed.
3. The fact he's alive, among the Shivans is important. Volition wouldn't end the first of two major storylines by saying "hey, shivans took bosch but they're just going to poke him it has not real consequences"
We know that subspace is relatively "fickle". The FS database tells us that most nodes open and close within milliseconds. We also know that larger nodes can be collapsed by way of large explosions, such as the sealing-off of the Sol-Delta Serpentis node by the destruction of the Lucifer, or the collapse of all nodes leading off Capella by Orion-class destroyers loaded with Meson warheads ("Clash of the Titans II"). Therefore, I feel it is not unreasonable to speculate that subspace damage is also incurred, on some level, by the use of subspace travel. It is entirely possible that traffic through subspace corridors will accelerate node collapse more quickly than the natural passage of time.
If the average subspace node lasts milliseconds, the lack of permanent subspace nodes would be the norm. Therefore, the collapse of subspace nodes by explosions or travel would also be moving things towards a more normal state of affairs.
Therefore, I'm unconvinced that travel through a subspace node has any effect whatsoever. Though certainly, the release of a massive amount of energy within a node will collapse it.
The Shivans do not "use" Knossos portals, per se. The portals exist in Shivan-controlled areas, but so far as we know, the Shivans do not know for certain how to activate them, or precisely what they are used for. It was Admiral Bosch who drew the Shivans' ire with his activation of the first Knossos;
This is an unfounded assumption. We do not know if the Knossos caused any emotional reaction whatsoever (negative or otherwise). What we do know, is that either from the Knossos' activation or from the appearance of the Trinity within the nebula, the Shivans began utilising the node and entering Gamma Draconis.
At the time of the SOC mission, only nine juggernauts had jumped into the unidentified binary system. Days later, when the armada gathered around Capella, that number had increased ninefold. This, of course, could be mere coincidence, but it could also be an indication that the objects destroyed by the SOC had more value than mere radio relay stations.
This is also a false assumption, in loop2-2 Snipes states:
Sathanas number six now in system. At this rate, we'll have a hundred Juggernauts bearing down on Capella in no time. Before destruction of the devices, the number of juggernauts moving in was already at the final levels. If anything, the number of Juggernauts DECREASED with the destruction of the devices because only 85 showed up instead of 100+. It's also safe to assume that since Snipes says it, Voltion means it. As I would think most in-game dialogue (cutscene or otherwise) has purpose behind it rather than just "this'll sound cool"
If true, it would mean that the SOC destroyed something far more vital than simple communications equipment. It would mean they destroyed installations absolutely vital to the Shivans' continued existence, and quite possibly killing an untold number of them by suddenly and abruptly severing their life support.
Furthermore, to refute the above, if the destruction of the devices killed untold numbers of Shivans, the assault would have been delayed would it not have?
The second, simpler reason is the simple fact that unlike the Shivans, Terran and Vasudan fleets actually make progress. So far as anyone knows, the Shivan species has remained essentially the same--if not stagnant--for the last eight thousand years, using the same kind of weaponry (as per the discoveries of the Vasudan scientists in Altair), and presumably, the same kinds of spacecraft.
This is completely false. A Lilith has a shivan turret in FS1, a LRed in FS2, isn't that progress?
The massing of the juggernaut fleet to destroy Capella must have one of two purposes: either as an offensive or defensive action.
Unfounded. Not everything the Shivans do must be offensive or defensive, there are more reasons than that. Take the Beleth, the Demon which was supporting the Sathanas, it didn't engage the Sobek but continued towards the node? Why? It had other things to do. Maybe the Shivans just had more important things to do than killing of the T/Vs just then.
We know that subspace is inherently unstable, both due to the brief formation/collapse of most nodes, and due to the fact that jump portals--once opened via jump drive--do not remain open for long, but quickly seal up after the vessel in question has entered the subspace corridor. If the Shivans are, in essence, living subspace energy, then their first explorers would have met a grotesque end, the very energy composing their beings dissipating and drifting off into the void.
The idea that Shivans are energy-based life forms is coherent with the FS Canon; the cutscene with the Shivans and what other references are made, fully back this idea almost 100%. If someone indeed thinks this is stupid perhaps they should play Freespace1/2 more often.
(above is from two posts)
If shivans are subspace beings, two questions need answering:
1. How does an energy being manipulate metal to make starships and space suits?
2. Why does an energy being need a space suit at all? They don't use ground troops? Why not simply have a solid spaceship and live as a part of the ship? Have a Sathanas as your space suit, that'll be more protective than some 2m tall thing. Energy beings don't need suits, and they don't need hallways to move around.
3. By quoting the text about the shivan weapon in Hall Fight, why is it assumed that the harnessing of energy to fire must mean it is an energy being? Do not lifeforms such as humans have energy as well? That's the entire basis of the Matrix triology. Perhaps the Shivans are simply advanced enough to harness their body energy.
1. "In the Lion's Den" is considered by many--including myself--to be the most compelling and exciting of all the Freespace missions. It provides a unique perspective from the cockpit of the Shivan Mara, an exhilirating intro ("DIVE, DIVE, DIVE!"), and witty commentary throughout by Snipes. It also gives the player the first real glance at Shivan "space", unobscured by thick nebular clouds. Wouldn't you think it somewhat anti-climactic, therefore, for the main targets in this mission to be little more than glorified satellite dishes?
2. Don't you think the Comm Nodes make unusually big bangs upon their destruction, if they are really simple communications equipment? The Alliance has studied Shivan comm systems before, but these give off "unusual" sensor readings before they go kablooey. Why?
I don't buy it. I don't buy the fact the a Comm Node, a defensive object in the middle of nowhere, is the lifeblood of Shivans in far off systems. I also don't agree with basing such importance on optional missions. Remember, that a player could play the campaign + skip these missions with the story still making sense. It makes sense in the Bosch case.
But since we're on the subject, here's my own hypothesis in short form:
A - the Shivans are a hive mind as suggested. They have a queen and a master hive, a Cyotus as you said.
B - Near the end of FS2, the Shivans were amassing a fleet to go and wipe out the Terrans. Even assuming they suspected a Colossus fleet, there's simply no reason for the Shivans to retreat by loosing barely more than 1 percent of their forces.
C - the Comm Nodes rather, are simply that: Communication Nodes. They have unusually high energies because they don't do system to system communication, but rather they connect the Shivan armada to main hive. By destroying the Comm Nodes, you destroy the link and the Shivan fleet is leaderless.
D - In the same way that Borg chick Seven of Nine yearned to return to the collective, so do the Shivans wish to return home to regain their link. The destruction of Capella was

a return, not a retreat, to the Shivan home base, whether it be an alternate dimension or otherwise.
E - so, while the end seems hopeless the player

saves the universe once again. By destroying a few comm nodes, he disrupts the communications and instead of the juggernauts annihilating all life they instead return home for some new orders.
F - By the same assumption, as a scouting force, the Lucifer fleet is expected to operate on its own. Therefore the Lucifer was the leader. Since there are no Lucifers in FS2, there are no leaders except at home base.
There you go