The initial version gave a lot of control to players, but had two main problems: from a player perspective those lovely shiny T2/T3 stations often turned out to be nothing but biowaste factories, and from a realism perspective the type of bodies was largely irrelevant, and only the space available mattered. I think this could be summarised as "not enough economic influence".
The second version addressed that by adding lots of inherent economic influence, so there were no more biowaste factories (to the extent that when I wanted to check something about colony markets I had to head back to the bubble to find one!). I don't think FDev realised how bad having mixed markets is, and I think we'd all agree that the problem now is "too much (mixed/unavoidable) economic influence".
The most recent update doesn't address economies at all.
@Tomsgalaxy is on the right track in wanting a way to limit where economic influences go, but I think there is a better way.
The initial version could be described as "colony ports get influence only from the local body" and the second as "colony ports get influence from everywhere". So why not have a choice available to the architect on each colony port of how far away the colony accepts influence from? Probably below the name change button? Then if you want it to work like the initial version you can select "local body" and if you want your T3 with no local slots to have an economy like the second version you can select "system". And it might make sense to have some extra choices like "local body and moons", "orbit", "star" (for systems with multiple stars) and maybe even "none". Default the choice to "system" and architects who don't go into detail will at least not get biowaste factories while more careful planners can get more careful results.
Economy overrides are a separate issue. To take the most egregious case, Earthlike worlds currently get burdened with four economies that all parasitise each other, so rather than being the shining jewels of the colonisation system they're muddy messes that produce random commodities (the only colonisation-relevant commodities guaranteed are some minor tech items) that change every time you build something else in the system. If my previous suggestion of influence range makes sense, then adding another option of which of the available body overrides to accept might also be appropriate. So a colony port orbiting an ELW could choose to focus on agricultural, tourism, high tech or military (or maybe even none, and get a different influence from facilities further afield?). Some might argue for being able to select multiples, but that would probably be too complicated. Or maybe "all" should also be an option, and be the default to keep behaviour as-is until changed? In any case all of the overrides should remain as boosts.
So the options would be
1. "Trade Range" selected from "none", "local body", "local body and moons", "orbit", "star" and "system"
2. "Planetary Economy" selected from "none", whatever the current available overrides are, and "all"
...with the defaults being the last choices in the lists.
And if someone really wants to have a port with a pure colony economy then they can have one!
I'm not sure when changes to these settings should be applied, and it doesn't make a huge amount of difference in the long run. Doing it at maintenance could push out the maintenance window, and a simpler solution might be to just zero all supply and demand whenever a change is made, and then just leave the standard supply/demand refresh to put the new economy into place. That'd also make it harder to exploit.
I'm not going to delve too deeply into specific instances of overrides, as I assume that terraformable bodies not necessarily getting a terraforming economy and non-terraformables getting one if they have organics is an oversight that will be corrected at some point.
TL;DR: If we add two architect choices to colony ports then everyone will be happy and people who don't check their settings will see no difference.