I'm absolutely with you on the base (assuming you mean the +X static job) buildings needing to be pushed to the general slots. But one of the reasons the extra build slots are attached to zones is because in the 3.1 system the more you generalise a planet the more resource boosters you need, and the more resource boosters you need the fewer spare building slots you have left over. This heavily incentivises specialising planets and a bunch of the economy changes are based around boosting generalised planets to be on about on par with (not better than) specialised ones. So unless giving single resource planets bonus build slots is the reason you want this combination of changes, just pushing the base buildings to general gets you what you want - building a zone unlocks the ability to build cool resources boosters, and you even get free slots to put them in instead of having to sacrifice a general slot.
Yep, that was the gist of my suggestion, I think. To be more detailed:
> The capitol area contains 6 building slots, although that might change due to policies, planet blockers, civics, and the like
---> It's pretty much like the latest beta build
> Planets might increase their building slots for each capital level/population level
---> Adding a more gradual planet development progression for all of us who like to play planet bonsai
> All "additive" & regular buildings that add a lump sum of jobs can be placed on all planets by default. Say, you don't need to unlock a specific zone in order to place a research lab or holotheater
--->
No need for specific research or factory districts; you can, however, fine-tune your planets if you need just a little extra sum of, say, consumer goods or amenities
> Each zone adds +1 regular building slot each and unlocks their advanced building/building upgrade. That is, if you would want to unlock a mineral purification planet or dimensional lab, you would need to unlock their zones first
---> I'm still unsure about whether building upgrades or building chains are the best option, but I am leaning more towards building upgrades in order to de-couple building slots from zones and avoid punishing mixed-output planets
This way, Zones get a stronger identity as tools for specializing both your planet
and buildings, you retain a more granular control of jobs via regular building slots, all while avoiding the "non-choices" presented by the "you can only put 3 possible buildings here", and the confusion created by buildings that you might place at any zone, thus breaking its own rules of the system.
Alternatively, another possible option for ending would be:
> Planets unlock regular building slots by ye olde good way (capital level, urban districts, etc, etc)
---> Because why change what ain't broke?
> All buildings could be placed on pretty much every planet
---> No "must have" zone
> However, zones, in addition to adding jobs to their district, would come each with a "zone building slot" (!)
> Only "zone buildings" might go into a "zone building slot"
> Rather than reusing old buildings and giving you limited options to place them, zone buildings would be brand new, non-tech-dependent buildings that add extra bonuses to the districts and jobs affected by their zones. For example, a "garden" might be placed in your agricultural district, so all your agricultural districts now generate a small amount of entertainers in addition to farmers
While that would demand the creation of a lot of extra content that would need to be balanced (at the very least, say, 3 different zone building choices per zone), that system would add a new development layer to your planets, allow for a more granular control of jobs, make mixed output planets far more viable, and play with many civics / unique planet stuff
TLDR: The non-choice of "you can only build 3 planet-unique buildings on their specific 3 building slots" must be removed in one way or another for zones to flourish, and that might possible entail the total or partial de-coupling of building slots from zones