Could it be that the Shivans are some sort of hybrid Von Nueman machine? I don't know if this theory has been covered or not but this is my theory:
(before you launch into reading this, I recommend
http://en.wikipedia.org/wiki/Self-replicating_spacecraft and
http://en.wikipedia.org/wiki/Self-replicating_machine)
Basically, we know from the tech room and description towards the end of FS2 that the Shivans are partly biological and technological, they are uber-destructive in the course of achieving their goal, there are A LOT of them, and they have been around for thousands of years.
From this, I would deduct/assume the following:
1. the biotechnology means they were either 'built' by way of genetic modification by something else, or they are an advanced enough to race to bioengineer themselves. 2. Whatever this goal is, it is some sort of prime directive - they accordingly follow nothing else by way of surrender or peacemaking efforts. 3. Their population being so high, I would assume either a massive string of overpopulated colonies to give host to the pilots, or that they are being constructed. 4. The sheer age of them gives me some indication that they have an extended history with the universe, yet their origins have to lie somewhere within it.
Continuing the thought process, I'm considering the technology aspect of it, comparing it with what else I know. The apparently endless population, the singular drive for something; could the Shivans be a race of Von-Neumann-like machines, albeit exceptionally complex? A self-replication machine would be constructed with only few directives in mind - the main two being (mostly likely) to reproduce and explore. If we take the results of the reproduce and explore idea many years after the point of construction, the machines would have a vast population and also an incredible knowledge of how space works.
For example. Imagine each machine created were given the directive of create 2 more machines and explore 10km^3 of space per generation. The first generation would have 1 machine and explore 10km^3. That one would spawn 2 more, who would each explore 10km^3. So for the second generation, we would have 2 new ships and 20km^3 more explored. For the third, we would have 4 new ships and another 40km^3 explored, totalling 7 ships/machines and 70km^3 explored. Each generation could be manufactured very quickly, depending on resources and technlogy. In a well stocked area, new generations could be built in a day. Given the number of days in a year and the number of years the Shivans have existed, it explains the massive population of apparently expendable machines. And this is only given the constraints. If machines were given directives to reproduce and explore infinitely, the population would tend towards infinity even faster.
The von-nuemann assumption explains a few aspects of their existence perfectly, as they have had millenia to replicate and explore, resulting in the incredible force the Terrans enounter in the games.
However, that assumption doesn't account specifically for the different types of craft we encounter, nor their origins, and I think for insight into this we have to guess a lot more:
So, the second half of my von nuemann theory is that what if an ancient species (not necessarily The Ancients, though that is possible) built the Shivans with purposes of defending or exploration. But that species was advanced enough to program their defense/exploration craft to evolve over time; to self-improve the self-replication.
This would explain the way they evolve - that its in their programming to not only (as we assume) replicate and explore, but also to defend and in turn evolve.
Could the Shivans be an advanced race of self-replicating machines that have evolved not entirely dissimilar to the human race (i.e. different types of spacecraft, pilots, weaponry, planetary takeovers)?
The final question to this is who made them and what happened to them? Again, working through assumption, we don't know who made them, but that species is most likely extinct, disturbingly at the hands of their own creations: The Shivans replication cycles and directives got out of control and they result in destroying their creators in light of their own objectives. This idea would explain why no other such 'origins' race has been found, and is a strong arguing point for the "Ancients built the Shivan's" idea.
I think the von-nuemann theory certainly covers most of the bases, but there are other possibilities.
For example, the Shivans may have engineered themselves to become what they are today; there might be no 'origins' race and instead the Shivans have bioengineered themselves to become the biotechnological entity that they now are. Since they are dated as being in an extraterrestrial war against the Ancients, they were at least as developed as the Terrans of the game, but thousands of years prior. Over all that time, the Shivans must have continued their technological advancement to such a level where the improvements to their technology were best implemented through biotechnology. In turn, they may have developed psychically to produce this apparent hive mind effect (Though keeping in mind the hive mind status is probably flexible - whether it is simply a awareness or a full communication is unclear, though more likely the former due to the fact that they still have technological communications). In conclusion, this alternative idea would certainly explain their existence more lucidly, but it doesn't necessarily hit all the targets.
Please comment/constructively critisize on those strands of my thinking, I'd like to develop the ideas further.
