While I agree the economy is indeed more shallow and convoluted than it is complex and deep, I believe many of the recent changes in 3.0 were made to address the balance between the simple (machine) economies and the complex (consumer goods) ones while still retaining what makes them unique and fun to play. Despite some aspects like logistic growth being a bit awkward, the overall effect has actually been quite successful. The general balance between normal empires, machine empires, and hive minds is definitely in a better place than it was before.
The one major outlier is ME Shattered Ring. As another poster mentioned in this thread, Resource Consolidation is actually in a very good spot - a bit weaker than Necrophage and VD, but right behind it in the next group of origins. The almost infinite scaling that comes with Shattered Ring just takes everything that is good about current machine empires and turns it up to 11.
In short, part of what is good about machine empires is the fact that they don't have to deal with the more intensive and convoluted economy that the non-gestalts have. That was the point of the original message I wrote, and why I don't think that Design Issue 4: The AI is the issue deserving of the most focus. It is taken for granted in every patch that some improvements will be made to the AI as the Paradox team devote more programming time to the game. Stefan ranks Shattered Ring for non-Gestalts as two tiers below ME:SR.
In your posts, for instance, you say that even with a 2250s Megastructure, you're still playing as a ME, not a non-gestalt. It's not SR that is the problem, but the combination of SR with ME.
I think the four mentioned economic advantages are relatively more important. Especially as the game still needs relative power differentials. A better AI wouldn't solve the problem experienced - Stefan only encounters three or four AI or so in that video, one of which is neutral, and two of which he is stronger than. It would be spectacularly bad for gameplay if relative power differentials didn't emerge - if every empire has the same power curve and warfare becomes impossible because there is no way to gain an early advantage over an opponent, either to outright conquer or to vassalise them.
And if the other four design issues are solved, the problem of ME:Shattered Ring would basically completely disappear because it wouldn't be possible to rush as many researcher jobs on a Shattered Ring while relying so heavily on the internal market to solve all the resulting problems, such as insufficient energy, insufficient gases, insufficient mineral production, etc.
It would be much better gameplay-wise if resources were conserved on the map such that if I am overproducing alloys and selling them for consumer goods, that consumer goods production exists somewhere else on the map to be sold back to me.