Zones are going to be a touchy subject, I think partly because there's no consensus on what they SHOULD be doing. They seem to be trying to fix a problem that didn't exist, and so it's kind of hard to pin down the precise point of what the new District/Zone/Building dynamic does compared to the old system. I know they elude to some bigger future use for them, but since it's currently not the future we have to judge them only as is and not some hypothetical "might be".
As for what's good: I think some of the basic idea is good. The idea of "building your own City District" with Zones and Buildings is neat and I like it.
As for what needs to be fixed: I think a lot of it. Not the entire system, as again I think the general idea of it is fine, but how it's implemented leaves a lot to be desired.
One big concern people have is that the new system floods the City District with too many jobs. If we compare the old and new systems we can see how bad that can actually get. In the most current build, 180 seems to be the "default" job number you will see on Zones and Buildings that provide jobs. We can easily compare this to 2 Jobs that was the standard for most Districts and Buildings. With some exceptions, most of the time if you built a new District or Building, you were creating 2 Jobs. Now with three Zones in your City District you are creating 540 Jobs, which would be the equivalent of creating 6 Jobs in the previous version. This creates a huge influx of jobs on any Planet focusing on non-Basic Resources, but a lot of the way the game plays has not been fleshed out enough to fully handle this change.
This leads into a second problem I have brought up multiple times in the Open Beta threads, and in the Survey. Buildings like Holo-Theaters still offer a flat amount of jobs of 180. And unlike the current system, Buildings don't seem to be upgradable now as most of the old upgrades are separate Buildings that do not add even more jobs. Though even if they DID add more jobs it would cause separate issues (Which will be discussed below). So while previously if you needed Amenities you could throw down a Holo-Theater that would give you 2 Jobs that would increase as the game goes on, now that single Planet Limit 1 Holo-Theater has to provide Amenities for your even larger job pools (As talked about above) while still giving the equivalent of 2 Jobs. This is true for any similar Building like Precincts, Gene Clinics, ect. This is more difficult to fix because you either have to drastically increase the number of jobs those Buildings give (Which isn't a great solution), increase the Output (A better but still not ideal solution) or make things like Amenities easier to come by from other sources besides Zones.
A third problem with this new system is that Building Slots are still too precious to limit the way they have. You get two Building Slots on your Capital Zone that are less restrictive, at least for now. You then get three Building Slots on each of your other Zones, which are heavily restrictive except for the Urban Zone, though they said in the Dev Diary that that will change. Every Ascension Path has a required Building. Robot Factories, Augmentation Centers, Cloning Vats, Psi-Corps, ect. So that's one of your two Capital Zone building slots down already. If you're using Organics plus Robots, that's your second Building Slot gone already. If you're playing an Origin or Civic that gives you a special Building (like Gaia Seeders), that's another of your two Building Slots gone. Restricting what you build in the Zones does nothing to help the game, especially when there's so few buildings for the specialized Zones that you don't even really need to make a choice. Picking between having nothing in a Zone, or putting the only option you have in the Building Slot isn't a meaningful decision.
A lot of this makes planets feel like customizable than before. There are just objectively less things you can do with a planet when it's so heavily restricted. As most Buildings are only allowed to be placed in their Zone, the only REAL choice your making is what three Zones to pick. Where as before you had 12 Building Slots to play around with, you now have three Zones and then the Building Slots are limited amount of passive buffs you can slot in.
The easiest solution, while keeping the idea behind District/Zones/Buildings alive is to shrink the number of jobs from Buildings by quite a bit, take away most restrictions (Switching Planet Limit 1 to Zone Limit 1 in most cases), and then have those Building's Jobs scale with Districts like Zones do, maybe even replacing some of the Zone's jobs with the new Building Jobs. This solves most issues, except the first issue of City Districts providing too many jobs. Though I honestly don't think there's a way to fix that issue with the system we're getting. In this scenario though, your jobs will never be outpaced by the amount of jobs the District creates, as it will also scale per District. You won't be fighting for the very limited space you have. You can make actual choices about whether you want to put a Research Lab in your Research Zone to increase Researcher Output, or if you are willing to sacrifice that Output to add in a Holo-Theater to start providing some much needed Amenities to your Planet. If you would rather have a Fortress for some extra Naval Cap (and Unity if you're playing something like Citizen Service) then extra Bureaucrat Output, then why shouldn't this be allowed?
If they don't want to go that indepth, they need to at the very least add more Building Slots to your Capital Zone, maybe unlocked through upgrading your Capital Building as you used to do.
We have about 4 weeks before 4.0, which is not alot of time. There's a lot of UI clean up, number tweaking, ect that they need to do. But none of that will matter if Planet Development is simply not fun for players. Some people in this thread seem to like the change, and that's fine. I want Zones to stay too. It's a good idea with a bad implementation currently, as it takes away player agency in how they want to build their planets. I hope these 4 weeks until 4.0 is enough time for the Developers, because I really want it to be the best it can be, especially since the DLC announcements look amazing. Until then, as much as it will feel like beating a dead horse, I think those of us who have criticisms of the change need to continue to be vocal about it.