I also think they shouldn't have tried to change so much all at once. Especially under these circumstances. Rather than having gradual change and working on one system after another.
They could and should have staggered the changes.
Change the job and pop numbers, because that will actually matter with Biogenesis. Probably making all buildings unique too, but without adding any new ones yet. More district types. Possibly restrict total buildings a little so you won't have all of them everywhere.
I refuse to engage with the red herring that adding more district types would be a ton of work. Just add one page in planet view for districts only with all the types.
Subsequent to the 4.0 release, they THEN could have tried a Zones beta. It would have had months before the next release, which is to say plenty of time to make it work well, and as it would include nothing else there wouldn't be any reason at all to keep if it they couldn't make it work. There still isn't, it's more work to make Zones work than to make every other part of this system work without them from right now, but even less.
IF the system as adjusted then made mixed output work better, THEN they could have tried the new trade system after that. The trade system as of now is based on the assumption that mixed output planets are more of an option. This assumption is currently false.
The trade rework assumes the economic rework made mixed output viable, which it didn't. The economic rework assumes Zones have helped, which they don't (hinder, actually, at the moment). The Zone system assumes districts wouldn't work as well, which is so far true EXCLUSIVELY for Betharian, which is a problem introduced in this very same beta.
It's like setting a bomb and then pretending you saved everyone when you defuse it too. Betharian is a problem because of the beta making it a Zone. Zones are necessary because the Betharian Zone doesn't work without them. So just make it a building doing the exact same thing and then try it as a Zone later, in a Zone beta.
This is all hypothetical, because that's obviously not happening, but it's what they should have done instead of this. If they didn't have enough time to do proper QA, stop the feature-creep and keep it to just the pop granularity, workforce and performance improvements.