Maybe the homeworld should be split into sub-sectors with various exclusion rules that denies certain combinations of outposts/unit spawns.
Basically, I think the game can already do this by the way.
First stage
Outer defenses -> Next jump is in the center, guarded by a core forcefield, the generator is in this outer sector, protected by outpost etc.. So basically you have to kill or hack/or whatever you do to disable things and then proceed to the next stage
Inner-sector is basically you enter from the center, there are 5 protection outposts at the 5 corners of a circle centered on the entrance warp-point. You kill those and back in Stage 1 a new wormhole spawns, that leads you directly to the core command station (now unshielded). (expand with secondary security systems as you wish depending on AI type)
This way you could have certainty that nothing extremely imbalanced will be grouped together. Also NOTHING on those 3 stages will ever leave it's stages to hunt you down (unless you destroy the AI home station). But entering 1 alerts all 3 stages for eternity.
Feasible for a patch?
Well... probably not. But it'd be nice to have some kind of structure to the assault. Currently it's more like a grind.