I like the plan that blueprints are learned faction wide, and aren't stored anywhere that the player has to worry about. If they were planet by planet, bound to those planets and could be lost, that would create certain incentives. I think my initial plan would involve maximized planetary defense, maximized heavy industry/shipyards, and a few expendable resource colonies in or out-system to feed it. I'd also make sure to plant several (ideally 5+) more mostly self-sufficient colonies around the system to spam more defense and patrol fleets out to bog down attackers further. I'd gamble on the fleet output by the high end planet to provide enough backbone for the spam to make the system largely self-defending, or at least enough to manage to defend itself for me to return to handle especially problematic sorts. Also, no AI Cores allowed in that system. Even in storage. Mostly because losing all my hard-gained blueprints would be an...unacceptable outcome.
Speaking of, patrol fleets. It seems that larger planets don't send out patrols to aid more isolated planets in other systems where they probably should. It'd make sense, or be appreciated depending on Alpha Core RNG doing Bad Things (TM) to colonies, to be able to have one colony send patrols to another's defense (ideally to be done automatically, really, especially with same-faction colonies in the same system). Also, on that note, it'd also make sense if the player faction goes carrier heavy, factions at war with them would increase the number of anti-fighter ships in their compositions. And vice versa for capital ships, etc. Maybe something to think about for two or three releases from now since fleet composition is going to be adjustable in-game. Granted, each faction would have 'preferred' fleet comps to default to even if they change in response to enemy doctrine, but it'd increase vanilla variety especially after the AI factions have fought a few wars with each other.
The apparent continued existence of marines alongside Alpha Core administrators doing *something* to colonies leads me to suspect that there'll be a reconquest mechanic implemented on Alpha Core colonies. Couple that with a population loss during the rebellion and an immigration malus for a time afterwards, and it'd be a proportionate disincentive to simply slap Alphas on everything. Permanently losing colonies with Alphas in play on, what seems to be sold as, bad RNG just seems a bit too harsh to be plausible to me. Or I'd find a way to mod it out, because that would just be uncool.