Having played through most of an AS game now, here are my personal suggestions:
First, Ancient Shadows is awesome. The Champion(s) suck up your excess attention like mercs do your excess resources.
A new quest, and a big reward for completing all of them:
Resistance is under attack: The deep space corps of the AI has finally gotten to the resistance bases. Save them and gain the ability to call in resistance strikes (1 per 2 hours, AI homeworlds exempt).
If all quests end in victory: you get to build the Shadow Hub. It connects all the backwaters to each other, and gives all of your ships the shadow drive.
Could you give the Frigate some usefulness after you unlock the destroyer? Like cloaking?
For directly triggered abilities, a shortcut I would really like, and which sounds easy to implement (like most things, until you try) would be a missile silo module, which generates AIP-free mini-warheads of its mark, with a high recharge time. These would have about 1/3-1/4 the effectiveness of normal warheads.
Refinement/feedback welcome.
Outright rejection less welcome but acceptable.