For chapter 1, having a company (with only a few thousand employees) declare war on the GTVA is bonkers, as is the idea that the employees would just go along with it. And them having SEVERAL super technologies.
A few remarks:
- "Going to war is bonkers for a company": That depends on their goal. You seem to assume that they wanted to overthrow the GTVA. The would indeed be unrealistic, even in its weakened state. But I can say this much without going too far into spoiler territory: That wasn't their actual goal.
- "employees wouldn't just all go along": No, they wouldn't and it was never the assumption that all of them did participate voluntarily. But if history has shown us one thing, both in RL and in FS, then it's that it only takes one somewhat charismatic and convincing leader who can sell an idea to get a lot of people to join him, even (and that's the shocking part) if those goals fundamentally go against the interests of the followers.
- "too many super technologies": The GTVA itself has shown a tendency of incredible technological leaps several times during FS1 and 2. It would also seem they've become really good at adapting Shivan technology. During FS1 it took them mere days to analyze and adapt the Shivan shield tech for Terran and Vasudan ships. After the Great War they managed to build their own beam cannons rather quickly. Meson bombs, ETAK, the tachyon technology of AWACS ships, etc. All those leaps have to come from somewhere. So, is it really that far fetched that those R&D think tanks may hold some things back if they're boss has a hidden agenda?
For chapter 2, I really didn't feel invested in the missions. Small militas that fly old rustbuckets aren't exciting to fight. Narratively, why would the militas that can't even afford a cruiser attack the GTVA? We are basically killing anti-pirate militas that formed for lack of GTVA presence because the GTVA is worried they might grow too big. Certainly not heroic. Perhaps it personal preference, but I still haven't finished chapter 2.
I guess that is indeed a case of personal preference. But I was very clear from the very first mission of chapter 1 that I don't believe that the entire life of a fighter pilot has to be one single blaze of glory. Sometimes (maybe even most times) it's just doing what needs to be done.
Regarding the militias: It's not just the fear of an outright attack that leads to them being a target, it's also what they represent. The systems in which they operate have been the point of origin of a rebellion before, and the mindset that fueled that rebellion didn't just vanish in the nebula with Admiral Bosch. The whole point of my campaign is to show how many cracks the GTVA already has when it comes to the collective psyche of its population. These are weak points that could be exploited. As stated above: You only need the wrong leader to go down a very dark path. So yes, while shooting down old rust buckets may not be too glorious or heroic, when it needs to be done, it has to be done to prevent cracks in the GTVA from getting too wide.