I like to think of the Shivans as being part of something much bigger than what we're presented with ingame. After all, we know that the Ancients alone encountered multiple senitent species - that, to me, suggests that intelligent, technological life is pretty common in the FS universe. Possibly there are species out there that coexist with the Shivans, maybe nit peacefully, but at least
safely, in some kind of perpetual stalemate.
I imagine the Shivans as being some kind of cosmic test - a complex one, and they probably didn't start out that way but that's what they've become. Figure out how to survive against the Shivans, and you enter the greater galactic community. Note "survive" as opposed to "defeat" - you might beatt hem militarily, but you might also hide from them (either by getting off the subspace network or some other way), run from them (convert your civ into some kind of mobile diaspora) or some other creative way. Frankly, there's no evidence for this in either game, but it does colour my perceptions of the Shivans a little.
So, in that context, I guess my answers would be along these lines:
Why do the Shivans want to wipe out everyone? (xenocidal "holy war"? remnant van neumann/self-replicating machines from some previous war?)
I don't think they're pure van neumann machines - particularly in FS1, they seemed to have more complex motivations that that - the infamous trap mission (Shell game was it?), for example, but we know they've been doing this for a long time - almost certainly much longer than the 8000 years we know about. This presents a quandry - frankly, if they were truly xenocidal, they could have been far more efficient at wiping out life in an 8000 year period - a few carefully selected stars would wipe out life over a 20+ LY radius - slow, if you want to kill everything in the galaxy, but faster than shooting them all one by one with beams.
In fact, as far as we know, the Shivans only target technological situations, and high tech ones at that. They left the Vasudans alone, despite the fact that they were a well established society (2000 years into Khonsu's dynasty at that point) of sentient beings when the Ancients (and therefore, the Shivans) were in the area. Why leave them alive? It would have been a simple matter to glass Vasuda prime when they took out the ancients, so, if you're truly xenocidal - why wait? There has to be some sort of trigger - something that a species does which gets the Shivans attention, which implies a degree of complexity to their motivations. I see two possibilities for the trigger - either by using subspace, or starting wars in space - either of them could be the cause or possibly both - the Shivans may be worried about the potential for node collapse if you bring your wars into their node netowrk?
Why did they blow up Capella? ("bridge building"? to get back home to "shivantown"?)
Frankly, Capella remains my biggest... not problem, but certainly mystery. The whole Shivantown idea seems... well, it certainly makes sense, and there's some pretty cool potential for storytelling if you elaborate on it, but... I dunno, it just doesn't satisfy me 100%. I think that the Shvans were portrayed very differently in FS1 and 2. For the FS2 Shivans, I can accept the "Shivantown" idea, even if I don't like it...but for the FS1 guys... hmm...
I guess the big problem I can see is the presence of the Gamma Drac nebula right next door (well, almost). Obviously, GD might be natural, but I just think that the combination of Nebula, then event which creates one is meant to lead us down the path of "The Shivans created the GD nebula". If they did make that nebula, wouldn't there already be a node to Shivantown, somewhere? Of course, it could have been a natural event... I have to go with "I don't know" on this one, interview notwithstanding.
How come they had beams and flak guns in FS2, but not in FS1?
I think they were different types of Shivans. The Lucifer fleet was a "scouting party" - a patrol fleet - cops, basically, IMO. They patrol space, looking for people who break the rules.
Anyway, the Sath fleet, by comparison, are the TRG. They're the guys who come in when things get too heavy for the beat cops, and you need some heavy weapons, although that doesn't explain Capella. Even more than the differences in weapons, though, the FS1 and 2 Shivans seemed very different - the FS2 guys seem much more van neumann-ey, for example. In fact, I wonder if the story writer changed between FS1 and 2? The stuff in the interview fits very well with FS2, not so much with FS1.
Personally, I suspect that while they are the same species as one another, they may be different castes or races or something. This would explain differences in weapons, as well as behaviour and (possibly) motivations.
Why did they capture Bosch and what did they do with him?
I have no problem with the interview explanation for this. I quite like the idea of Bosch being undone by hubris, kinda. All his grand plans hinged on speaking to the Shivans, and then he finally runs all the blockades, evades the GTVA, gets into the nebula and then... he gets ripped apart by angry shivans.
Why did they wait so long (32 years) to send reinforcements after the Lucifer was destroyed?
Maybe they didn't know something had gone wrong until the Lucy fleet failed to make it back to "Shivantown" after some pre-assigned patrol or scouting route in some 50 odd year cycle? Or maybe the Shivans just work on a vastly different timescale than we do, and 32 years was just how long it took to respond? Maybe they were growing/building the Saths in that time (although personally, I don't like that idea... again, it really just doesn't sit right, the Saths should be old).
Again, personal view here (and leaving aside the obvious answer of the plot needing time for the GTVA to recover and develop technologically in order to make the second game sufficiently unique and fun

), I suspect that the 32 years was some kind of programed response. If the Shivans were on a scouting or patrol trip, we have to assume that it was on some kind of long period - they'd been here 8000 years ago, then an unknown number of times between then and now, looking for people whome they needed to wipe out. I personally think that there are multiple Lucy fleets on massive, long term scouting paths, 40 or 50 year voyages - when one doesnlt come back, the Shivans initiate a
response.
Why did they wait so long to wipe out the Ancients?
Well, we have no timeline for the Ancients. The FS1 cutscenes seem to suggest a link between subspace and the shivans, i.e. entering subspace caused the Shivans to come for them, but it also seems that the Shivans took awghile for the Terrans (at least 14 years of subspace use, probably more, since I doubt the TV War started as soon as the GTA pked their head ou of Sol). Plus the Vasudans were supposedly out even longer thant Terrans. Again, I think it's the combination of war and subspace which attracts the Shivans, and there's a lag time of at least a couple of decades (possibly related to how long it takes for a Lucifer fleet to find you?)
How long have they been at it?
Long enough that their behaviour has become predictable enough to be a test (although that's based on nothing more than my own theories). I think that the general consensus is that they've been at it a long time, possibly into the millions of years (although I tend to think less grandly that that - if I had to throw a number on it, I'd go with 25000, maybe 50 as an upper limit, although again there is zero evidence for this one way or the other, except that the entire galaxy hasn't been in some way "Shivanified", which I would expect for million year scale timelines.
What were those Comm Nodes for, anyway?
Honestly, I don't thiink they had any deep story purpose. When you're FREDding, I know how difficult it is to come up with stuff to keep the player occupied during exosition missions. You can't give him too much combat on what was meant to be a stealth mission, so you need another distraction. Enter the commnode - a very odd-looking, very non-specific prop that behaves unusually enough (the centre crystal) to keep Alpha 1's attention while -[V] tell their story.
There are lots of ways they
could be worked in at some deeper evel, but honestly, I think anywhere [V] went with them would have been after the fact. I honestly think the only thing they were for was to give the player something very slightly original to do in those few minutes they're on screen.
Will respond to some other people later.