1,2: Opening one subspace node doesn't incur the wrath of the Shivans. It's more likely that extended overuse of subspace does. E. g. the 14 year war, or the ancients expansion (as we are led to believe in FS1). However IIRC it's mentioned somewhere in FS2 (in-game dialog) that the portal leads to the area of space where the ancients first encountered the shivans. Of course it does. The ancients activated at least 3 portals. The shivans immediately responded. Maybe their expansion was not enough to summon the Shivans.
Then the Ancients quickly retreated. They didn't bother to close down every Knossos, only the first one, as they didn't have time/thought that was sufficient. But what they didn't know was that Shivans could enter normal space elsewhere (like Ross 128)
3/1: Perhaps because the plan was devised after his rebellion? When the Shivan Saths started pouring into Capella.
3/2: So if their goal was to prevent the GTVA from sealing off Capella, why did they decide to blow up the star, which IMO destroys the nodes as well? And makes travel to that system problematic because the new nebula is a little too hot even for Shivan armor
3/4: It is, but even if they are not, their physiology is likely different enough to make communication problematic. They communicate in quantum pulses, after all.
3/5: Heavy fire? I don't call that heavy fire when there's 80+ Saths in the system. And I'm not saying that the Shivans' priority at that time was defense of subspace. It was second. Their priority was getting home. As for the Vega-Capella node attack, that was just the standard Shivan "control of subspace nodes" behaviour
1)2) Again wholly assumptative. Why would the Shivans not attack again in the many. many years following the Great War then, if it was down to simple long term use? I find it unlikely destroying the Lucifer would give the GTVA a 'clean slate' from the Shivans. Also, why would the Ancients take a strategy that entailed losing 2 systems by activating the 3rd Knossos, when activating the 1st (Lions Den) would lose no systems? It would seem simple logic to shut down the first Knossos possible, even if just to allow a longer fallback. I will concede, though, that the Ancients could have believed they could have recaptured that system in counterattacks.
3)1) I doubt that; the GTVA would have a responsibility to plan for the Shivan attack, and would also have surely studied the whole issue of collapsing a node after the Sol node was destroyed. In any case, it would be obvious once the GTVA destroyed the knossos. Even if the Shivans - unlikely - couldn't figure that out, Bosch sure as hell could.
3)2) That's exactly my point RE: protecting subspace and humanity as a whole. If they wanted to protect subspace from GTVA damage, it was piss easy for them to do so. It becomes obvious that whatever they wanted to do with Capella - whether or not that was achieved - was more important than a piddly little alliance, and that draws into question whether humanity was really doing anything damaging enough to attract the Shivans.
3)4) Problematic does not mean impossible, and the Shivans are a somewhat capable race. It would appear quantum-pulse comms is not beyond humanity, and the Shivans... well, they're an order of magnitude ahead.
3)5) The messages in that mission indicate the pilots considered the prolonged Shivan attack upon the Bastion to be heavy. The player, after all, only comes in quite late to assist. Also, the Sathani may not be intended as that type of front line warship; perhaps they have another primary purpose (to do with the nova) - or are simply too slow.
You're assuming the Shivans were trying to 'get home', and indeed that the supernova was intentional to that effect (which begs a question as to whether a nova is 'good' for subspace)
Of course, there are many reasons for attacking the Vega-Capella node; providing a screen for the Sathani being one. But it's also common sense that the Shivans would anticipate the Vega node being destroyed (it would have been blindingly obvious, especially after EP was collapsed), so perhaps they are not all that concerned with 'saving' it. In either case, there's no basis for the assumption the Shivans did not know of the GTVA plans to destroy the nodes; the question is how much did they
care, and it's pretty obvious the answer is 'not much'.
As for the rest, I'm quoting the manifesto again:
c. If the Shivans are truly xenocidal, why did they respond to Admiral Bosch? What happened to him?
*snip*
The most plausible explanation is that the Shivans were more intrigued by the nature of Bosch's transmissions, rather than their actual content. Bosch himself states that the first contact was "rudimentary and crude", meaning that the content of his message may very well have been different than what he'd initially believed--something nonsensical like "cheese is ambitious except on Sunday in winter" as opposed to "we come in peace". The Shivans, in turn, would have been puzzled by what they encountered: a Shivan transmission emanating from a Terran vessel. When they investigated, perhaps expecting to find captured Shivans, but instead discovered an overly-idealistic Aken Bosch, it is reasonable to assume that they were none-too-pleased.
To conclude the point, Admiral Bosch is likely dead. After being presented with a vessel full of unprepared Terrans, the Shivans probably acted on the chance to conduct biological dissection and other experiments upon their new specimen.
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 kind.
Secondly is the problem of the language barrier itself. Humans aren't Shivan, as Commander Snipes so succintly points out to us, and we don't speak "quantum pulse" very well. So far as we know, the only ETAK prototype was aboard the Iceni; whether this device was destroyed along with the command frigate or not is unknown, but it can be assumed lost. ETAK was a prototype device, and as the first of its kind, probably wouldn't have been very portable. The first Earth computers were enormous, taking up entire rooms, and Bosch's ETAK may very well have existed on a similar scale.
Despite Bosch's rigorous study of the Shivans, he's no MacGyver, and it seems unlikely that he would be able to rebuild such a device completely from memory. Even if we accept that Bosch had the ETAK blueprints stored on his nifty little laptop, and that he took it with him when he was captured (something that is virtually guaranteed to be untrue; if the Alliance hadn't recovered Bosch's computer, then we probably wouldn't be reading his personal log), then he is still aboard a Shivan vessel, with no Terran tools or materials with which to assemble his device.
BTW I've discovered that a very big part of the manifesto is missing on the new server. However, I managed to find it in Google's cache. http://216.239.51.104/search?q=cache:QtdDGcsf77wJ:dynamic.gamespy.com/~freespace/forums/showthread.php%3Fthreadid%3D22279%26highlight%3Dmanifesto+area+of+space+where+the+ancients+first+encountered+the+shivans&hl=en
The ending part about the Shivan retreat, the idea that shivans damage subspace themselves, the conclusion -- it's all missing on this new server.
I consider the manifesto fairly meaningless as a source, and this is a good illustration why. It's ridden with assumptions because IMO it was likely wrote with the conclusion decided, and the question being how to crowbar in everything to fit.
In particular a translation error would be highly unlikely to provide such a correlative response as for the Shivans to know both where the Iceni was, who to grab off of it, and indeed that they could even board it atall. It would require an error that somehow preserved a consistent meaning that appeared differently to both sides; in reality the effect of a mistranslation would be either gibberish, or rapid divergence as misunderstood replies compounded prior errors. The assumption here is massive, and it runs contrary to basic translation logic. Even a simple 4-line experiment with similar languages in Babelfish would show this.
In terms of the Shivans taking prisoners; there's no attempt to explain why the Shivans took command crew for this purported experiment rather than just people in general. For Shivans to specifically target the commanding officers of the NTF implies some knowledge of the NTFs structure; moreso because they slaughtered most of the rest of the crew, meaning it's not a case of grabbing the first person they saw and buggering off.
Also, the Shivans did not destroy the Iceni after boarding it; why? If they didn't communicate with Bosch (who would need his command codes), how could they know self-destruct was commencing? Why did the Shivans use the airlock, when they can canonically survive in space and just tear through the hull in what would be a more sensible surprise attack (in order to rescue similarly vacuum proof comrades)? The only need to use the airlock, was not to kill the (human) people on board. Additionally, why would the Shivans take human prisoners now and never before? If they interpreted the ETAK signals as a distress call - something we have no evidence for believing an individual Shivan can do, especially given the specimens stored by the GTI in Silent Thread - then their view of humans can't have changed.
It's also worth noting that the only known human-Shivan meeting - Hallfight - had the humans fire
first.
There's no reason for the assumption we are 'reading' Bosch' log atall for the monologues - which is the only part that could mean - and it makes less sense in the narrative than simply regarding the cutscenes as interludes or cuts to a parallel part of the story. I'm sure atall what that line is meant to mean. Not to mention the fairly blatantly obvious possibility if we are reading Bosch' logs... perhaps they stored copies of their information on a central computer? Like pretty much every organized computer network of the modern day?
Also, the idea that the Shivans wouldn't have taken prisoners is based on a wholly unfounded assumption that communication had not been made. Which runs contrary to common sense and the obvious meaning of the last monologue and the GTVAs own intelligence of the ETAK device. We also do not know what the Shivan could or did take from the Iceni, and the idea they are incapable of making an ETAK style device is an equally unfounded assumption; not only do they have the highers up of the NTF (quite possibly including their chief technicians), all the Shivans would need is to understand the
principles to manufacture their own version.
And, of course, we have no idea how large ETAK is, how long the Shivans were docked, or even if ETAK itself is a physical device rather than a software program combined with rudimentary and scaleable existing technology. The assumptions regarding the size of it are completely - again - unfounded; a device based on a unique combination of components has no need to be large with a society as advanced as 24th century earth. It's worth noting the main reasons for the size of large computers was largely restrictions on the physical manufacture of components; by the era of FS2 the GTVA is capable of nanotechnology (according to an FS mailing list post by Adam Pletcher, IIRC). I'd wager myself that the largest part of ETAK would be the physical transmitter.
(also, it's not exactly bloody likely Bosch would leave the Iceni to go with the Shivans without a method of communication, is it?)