Thanks for the blog update. Couple of comments/wishes for it.
1: Give the player ability to *somehow* max the security so no raids/luddic path presence will affect the system with raids. Be it very heavy security presence for example (Stacking bonuses from several security buildings/stations on couple of the system planets) for example.
This way the player could choose to sacrificise some potential building slots or income via investments into system security so they would as you said, have to play whack-a mole a lot that we do with the existing system. The dev blog proposal does not really fix it so to say, merely changes it. We still have to deal with the pirates/luddic path/empire raids/AI investigation squads. This would also mean that players would/should/could have the ability to automate making sure the Luddic Path does not come snooping around AI colonies, for example by getting good relations with them and then perhaps having a constant bribe running with some Luddic path agent. Ditto for the empires, so empire raids could be deterred via good relations as its, frankly speaking pretty dumb that they come knocking "raiding" you just because you're doing well. Either declare war or do nothing, since the player can't exactly do the same to them without suffering massive relation penalties (nor is that the wanted option of this point).
2: Let players give Military Bases mission orders.
This has probably been a very requested feature. This would directly give the player a reason to upgrade to a military base (or perhaps 2 if more military bases mean stronger system fleets in the reworked system) since they could remotely (if the system had a comm satellite) give orders for military bases to go squash out a pirate/luddic/insert baddies here base. You already pay upkeep, perhaps those "operations" could cost a little bit of dosh ontop for gas fee or something but nothing extraordinary. That way the player still has to "deal" with the hostile presence if a player has invested into system security they could micromanage it to the system Military HQ's.