Jenna should not lead the Terran Alliance in custom games. As far as I understand the story at the point of discovering the hyperdrive she is not a prominent person (and at the end of the ToA campaign Earth is still completely isolated - the explosion only crippling Dreadlord and Arnor production/creation abilities).
The terran intensive farming tech should be split into two (to give one building level per tech).
Better store of created custom player race - after a while playing only with the defaults it seems my custom race setup is loost for me only appearing as a competitor.
Not so small but I would also like to be able to demolish super projects and super projects to be autodestroyed when taking over the colony.
Sligthly better explanations in the user guide, I still do not fully understand in the combat section at some points whether weapon means weapon category (ie beam) or weapon item, and no idea on the use of focus during design - by the way in focus one defense category seems mandatory.
Starbases take several dozens of constructors to fully build up, having more modules per ship would be good.
Tech-end weapons are too strong relative to both the previous level and the defenses.
Absolutely not small but I would like to see no default hyperdrives and sensors in ship hulls - so if someone designs a ship without a hyperdrive it will be a satellite, not able to go to the next planet (of course with a revision of speed bonuses and abilities). And also a serious revision of sizemods: Engines and supports really getting bigger (and if possible more expensive) for larger ships (ie 10 times as large for a huge than for a tiny), sensors and defenses getting slightly bigger (due to the larger inerference created by the hull itself and the larger area to defend by some of the methods) while weapons should retain size regardless of the hull size.
In "both sides killed" combat situation the starbases should receive the "survival hit point" instead of the attacker.
Probably not for an update but for the next incarnation, starships should loose modules, a huge ship with a single HP still have full attack capability. Not too realistic albeit very usefull for intercepting small Dreadlord waves.