another idea is having alts(and/or faction mates with alts) to spawn in and homebase protect your warpgate network
But that isn't really addressing the problem, and i think it's a problem with resources themselves. Without abundance there can be no infrastructure, without infrastructure there will be less abundance.
The NPC factions are a good start, but I hope future updates bring faction-control to player factions. creating faction fleets and bases to serve roles for each system comes to mind. Defense of structures, "free resources" to supply that.
We can designate a structure type when we save a blueprint, it might be worthwhile to do the same when you spawn an entity (like a space station). Giving player factions a similar system to the NPC ones certainly would promote building more emplacements of different types(for the faction-level bonus).
Example: designate a station an "outpost" and it counts as scanning for your faction, revealing cloaked units in the neighboring 8 sectors. Spawning "mining" stations gives you a flat bonus/station, factory a flat "universal production/turn", etc...
I suppose there would need to be an incentive to go against "floating faction modules" to exploit a peaceful system, perhapse a minimum target systems value(or percet) to be designated as one type or class of thing?