Ultimately the Faction VS Faction missions reminds me of Mario Kart and rubber-band AIs, or Homeworld 2. Not a good thing, and not entirely intuitive. From a personal perspective, I'd love to see it go entirely - I don't play sp with champions any more as I just don't find those missions fun. From a design perspective, I see the necessity of some method of preventing the domino effect.
While it is outside the scope of easy and practical to implement, I think the compensating increase in production would best be replaced by (one-time, repeatedly?) spawning a mini-boss, a not-quite nemesis. Same theoretical spike of difficulty, but a feeling that you're not in the same place you were before, and nowhere near the same chance of being overwhelmed by spiteful RNG spawning the right thing for your guys and the wrong thing for the enemy.
Aside from ally AI, one of the things I find contributes to the sense of futility (but isn't responsible for it) if I've gone in with the wrong strategy and tactics is the fact my Champion is slower than everything else in the nebula. I often cannot make it quite in time to shield the few ships that make it to the base, or draw fire with my shields, or cover the starbase. I can wait for them to arrive somewhere, but I just can never catch up. I wouldn't even object to nerfing just allied nebula starship speed so I could keep up. It's an escort mission where you can't even keep pace with the unit(s) you're trying to protect. And you're not really capable of interception either.
I'm afraid I'm not really capable of considering everything that goes into balancing these scenarios, and I can see some of the things I can do to beat them a bit smoother- but I'm just not motivated to do some of these scenarios when even getting that first level or two outside of the first nebula doesn't smooth things particularly. If I can have a painful time even when I optimize my modules before hand, learning how to solve these scenarios in suboptimal conditions falls in the realm of netflix, but I have to pay attention.