I wouldn't say the Shivans overstepped their bound with their first attack. After all there was the whole Terran-Vasudan war going on for decades. Without the Shivan intervention the most likely outcome would have been the eradication of one species and all that over a stupid error in translation....
The second Shivan incursion though is another matter. The NTF rebellion (apart from being an internal matter) was something the GTVA was capable of handling themselfs, even though they needed a long time for it. After all they were able to crush the rebels even while they were also busy exploring the nebula and battling the Shivans on a second front.
you could bring in some of Vishnu's thematic imagery for the Vishnans. Dark blue / stormcloud coloring and patterns, conch, wheel, and lotus shapes could make some truly interesting ships. The current line just doesn't fit the Vishnu/angelic theme as well as the shivan ships fit the Shiva/demonic theme.
Darius didn't make the Ancient/Vishnan models, he just re-used them. As far as I gathered he didn't know how to model back then (though he learned it since then - there was some comment about one of his ships being in WiH if I remember correctly, though I don't know anything more).
Upon reflection, back-engineering some of the later War in Heaven prose into Age of Aquarius and expanding the dialogue upon arrival in Sol might have improved the final mission.
Since you didn't play through the original release till the end you wouldn't know it, but they did that. The line about the GTVA believing the UEF to be "religious pacifists incapable of selfdefence" or somesuch was only addad with the directors cut. Also Renjians lines were a bit extended ("Desperata Ferro" for one thing wasn't in the original).
In the original Admiral Bei just says that the GTVA send them as an invasion force, but never goes into the reasons why command decided that.
Also there are very good reason why not all of the 14th battlegroup defect (apart form beliefing command point of view. Loyality being one. They all swore an oath to serve the GTVA and it's principles and obey their superious. That's the tricky part. If you swear two things in the same oath, and they come into conflict with each other, which one will you choose to follow?
Another would be, not wanting to fight against your comrades.
While going over to the UEF might seem like the right thing morally, it also means you will have to fight with your former comrades sooner or later. Against people who might beliefe as much as yourself that they do the right thing for the good of Humanity.
It's easy to blast some cruel, faceless enemy beyond Human understanding. It's quite another thing to blast Human beings. Even worse if they are people you know. And even worse, to know that, if not for a twist of fate (or Vishnan intervention) you wouldn't fight against but alongside that pilot you just shoot at.
So it's not really surprising that members of the 14th battlegroup would just do nothing and risk being court martialed rather than defecting.