Right now there's a bit of an issue that I have with the way the production chains are done.
For one, almost all the higher tier resources are made from minerals. Which is a shame. Consumer goods are good in that trade can give them as well but alloys, crystals, gasses, motes they're only made by either a direct tap that's kinda rare or you build refinery planets. I wish there were buildings that turned alloys into consumer goods or turned dark matter into energy or crystals into motes or motes into gasses or gasses into crystals. You already have a building that uses motes to make minerals and a building that turns minerals into motes...but there could be vastly complex resource chains and unique buildings or high tech buildings that do a lot more.
There will always be a split between primary production (resources extracted 'from nature') and secondary production (resources converted from other resources). However complicated you make the secondary production, it has to be limited somehow by your level of primary production.
If you create long paths where a short path already exist, e.g. minerals -> alloys -> CGs when minerals -> CGs is already possible, you create some nonsensical situations where compounding production bonuses mean that the long path has a much greater output just because of how long it is. Any sort of cycle of resources is a no-no as with sufficient bonuses, it would lead to an infinite resource machine that is divorced from any sort of natural input. So I think you'd have to be very careful in introducing unorthodox methods of converting resources and not making them too efficient.
Secondly, whenever I build a rural planet, where I just want minerals, energy and food I run into the issue that I need to go the full trade value clerk jobs route because there's nothing else for me to build into the building slots except hydroponic farms but it changes from rural to agri if I build to many of those and there's no mineral or energy building. Which I mean I get why there wouldn't be one specifically for them but you could have OTHER rural building types. There's not enough options for worker jobs for rural planets and you kinda need rural planets because there's not enough specialist jobs either, almost all specialists use minerals in some way, some use them in consumer goods form but those cost minerals to make so you cannot have too many specialist based planets without your mineral income tanking drastically. We need more buildings to fill out the gaps on both rural and urban planets.
I'm not sure if it would be a good idea to have mineral/energy versions of hydroponics farms, at least for non-Gestalt empires. If you can just stuff any planet you like with whatever kind of basic resource production, then the system of natural resource districts becomes meaningless.
In the current version, the rural planet bonus is so tiny that I wouldn't worry about it. You can build anything you like on a 'rural' planet; if it ceases to be 'rural', it's no great loss compared to the benefit of the buildings. You probably want to concentrate your labs on a small number of tech worlds with assisted research, and your alloys/CG factories on a few forge worlds; but once you've done that, all the other types of building can go wherever they fit. So I agree that more building types would help here, but they don't have to be specifically 'rural' building types.
One change that could be made though is to allow players to explicitly declare the specialism of the planet (maybe at a small Influence cost?), overriding whatever specialism the game generates automatically. There could then be techs etc that improve the planetary specialism bonuses.
Lastly, there's a bunch of high-end resources that have nearly no use. Living metal, dark matter and zro are pretty much useless for most of the game. Dark matter you don't have any way of using until you kill Fallen empires, despite you being able to "mine" it a LOT earlier than that. Living metal is only used for Megastructure build speed isn't it? There's no other use is there? Its kind of disappointing that the most valuable and rare resources are nigh-on useless. At least Crystals and Gasses and Motes have buildings that use them. What good are dark matter deposits if nothing uses it? There should be dark matter reactor buildings and Living metal factories and Zro unity buildings and stuff.
Definitely, there should be more interesting optional uses of these high-end resources, even if it's just a few more edicts. Zro is a special case because it's so strongly associated with psionic ascension, but certainly the average empire should get something out of dark matter, living metal and nanites.
Crystals/motes/gases are really in a different category: they're mid-game strategic resources that come into the picture at a certain level of technological and economic sophistication, like coal in the Industrial Revolution. I think they have a decent range of uses already, but I have a few gripes:
1. Given how integral to the overall economy they become in the mid-game, they ought to be displayed prominently at the top of the screen like minerals/energy/food/CGs/alloys are (at least if the player's screen resolution is large enough). The current setup where you need to look at a tooltip is a real nuisance.
2. Because of how critical these resources are for building up to high population densities, there needs to be some synthetic production option eventually, so I don't have a problem with chemists etc. What I don't like though is that the technology extract these resources from nature takes so long to appear, and then the tech to synthesize them comes almost immediately afterwards. I would like there to be a phase in the game of a few decades where you can make good use of any natural deposits, but can't synthesize rare resources, so that there's a reason to fight over the deposits and you have to decide carefully how to use your limited supply.
3. Dust caverns etc as rare planetary features are disappointing, for a similar reason. OK, so this planet has motes in it, say. But to get the motes, you have to build a building to extract the motes, and have a pop work it. What's the difference from just building a chemical plant? The main difference I can see is that the chemist eats 10 minerals whereas the mote harvester doesn't. So effectively what you're gaining is not motes at all, but rather 10 minerals, but it's a flat 10 minerals gained, not boosted by mining bonuses. On the scale of a planet, this is not very exciting. I think it would be better if instead, dust caverns were a special type of mining district, and the 2 miners working there produced motes in addition to their normal mineral production.