Just beat the mothership on stage 1. I took all off my marines and went 30/30/30. I never adjusted engineers and only sent for pilot refill once.
For research i went all 30 into physical,for a simple reason: more control over what I could get. Instead of having my researches scattered between bolter, laser, orb and plasma and their upgrades, plus shields, I had gattling and missiles.
Made 4 bolters and 4 hangars. Got missile research first and though I couldn't afford station launchers, I gave all my fighters missiles. I set them all to defensive, auto launch, shielded, evasive, target strongest, and target hangars 1st.
Gattlings researched second and I bided my time, replaced all 4 bolters with gattlings and eventually replaced all 4 gattlings with missiles.
Every wave a carrier spawned I set my fighters to aggressive, they made short work of the carrier, and i set them back to defensive. I also would select the big ships and tell my guys to focus, just in case.
Later on I bought a capital ship, set it to the left of my station and a missile ship at the right. That's it.
I noticed you can't give orders to fighters from a carrier/hijacked carrier/capital ship, so they just buzz around with bolters and get murdered, making them a waste of space and pilots. They were a minor distraction atbest in the final wave or two, when I threw everything I had at the mother ship.
So.. Suggestions? Here's a few...
1: Let you set fighter orders and layouts from carriers/capital ships too.
2: Different battlestation shields, like ones with a wide area which can help protect near by ships by taking the hits first. Maybe reinforced bulkheads as an option, which gives no shield, just adds more hp and maybe armor.
3: Allow ships to earn kills, giving them something like veteran then ace status, along with small boosts to overall performance. Im assuming from reading the kickstarter page that your adding commanders with their own traits and levels and such so I'm referring to minor ships.
4: Allow commanders of some kind to be set over fighters, piloting a stronger fighter, which will let the squads performance be boosted, maybe even add flight formations and attack patterns as their skills increase. Strafing could be for damaging ships and dogfighting for fighters.
5: In addition to big ships, allow small ships, maybe ai controlled with the same options as fighters, similar to the different varieties that attack the battlestation. Maybe a scavanger could be one of the station modules and lt you gather resources for this purpose.