I would not be surprised if Alex fixes this by making AI steal your (excess) colonies and turn them into more Remnant generators, (fix and) buff zombie Pathers to do worse things to AI colonies, or make inspections too frequent to bribe away (although that one can be fixed by wiping Hegemony off the map.)
If not for bugged Pathers, I do not know if I would abuse AI cores. I avoided Pathers at all costs to keep zombie chasing down to barely tolerable levels instead of intolerable. I sunk a ton of points in Industry just to have colonies and avoid Pathers (before I knew about the Pather bug). In the end, that gutted my character's combat power, and I wished I could respec those points away (probably for armor skills and officer management). If I play another game, I would totally ignore Industry and abuse cores.
My biggest problem with non-AI use is it is impossible to colonize the sector. At best, you get up to seven or eight colonies with full blown colony skill investment. If player wants to colonize hundreds of worlds and become space emperor, alpha cores is the only way. Close runner-up is full colony skills guts combat power too much (by taking nine to twelve skill points away from combat).
P.S. If colonizing the map is undesired, then there should be limits AI can be used safely, more than that and excess AI will turn rogue and steal your worlds or something equally sinister.
I think the administrators skill should improve them and the limits of administrators should be removed. That would be a good start.
Maybe spend story point to upgrade an admin?