Not sure how much of this should be in spoiler tags so I'm going to put the lot in:
Something I've been trying to wrap my head around that is bugging me is Ken's contradicting motivations. For instance, it was Ken himself who informs you in Act 3 that the GTVA are essentially trying to eliminate Vishnan-influenced elements in Sol (or at least that's how I interpreted it). But this is a good thing. This should play right into his hands, or the Shivan's hands I should say. It might not be clear what Ken's end-goal is, but one thing that seems to be pretty clear is that he is thouroughly anti-Vishnan. (I say 'he', 'it' would probably be a better descriptor).
So why then does Ken directly instruct you in part 1 to "destroy the GTVA"? I found it really weird when he says this, not least because as a Shivan metamind the success or failure of one trivial human faction in a trivial war seems completely inconsequential (relative to him). Asides from that, assuming he actually gives a crap he should want the GTVA to win and steer Sol and the rest of humanity away from Vishnan influence (if that's even possible).
One thought I had was that the element of Ken that is Aken Bosch is still prejudiced against the GTVA and wants to destroy it, but that seems far too narrow-minded and pointless. It got me thinking though, how exactly does a Human-Shivan metamind work? Is it possible it can suffer from split personalities, each with different goals that can potentially conflict with one another? Perhaps the fragility of a human consciousness can cause the metamind to hiccup every once in a while. I'm sure we'll see in the end that Ken ultimately has a goal and a plan to achieve it, but I kind of like the idea that a Shivan can be made susceptible to human error.
I was sure from the beginning that the GTVA had much stronger motives for going to war than just for the lulz and Act 3 pretty much confirmed it for me. It's sad because the UEF is obviously the much more stable, evolved society, but that its
Vishnan infection
has pretty much tainted it.