Personally, Devs, I'd like to see a series of procedurally generated z levels, even with an option to build upwards like a skyscraper or something. I think this would add a depth that, (no offense) has been lacking for a little while, but I would also like to caution you against making this Z level system too complex, as it would detract from Factorio's beautiful contrast of simplicity in theory and complexity in reality. I guess a good way to go about this Z level system would be to have several different aboveground layers, which would allow for mountains to be created to give the game a slightly more realistic feel, but at the same time keeping the amount of mountains generated to a controlled level where you have plenty of room to build factories on plains, (Like you do now) but mountains to build on and mine in, generally confined to mountain ranges with a few loose mountains here and there.. I personally think that the aboveground ore deposits are a good way to go about things, but I think you should make mines in mountains have a higher yield, albeit a slower mining speed until you upgrade your mining technology. and have the Z system work like this:
*Mountains which range from small hills to Mt. Everest
*A digging system which allows you to enter belowground levels via constructing a mineshaft, or other entry method, and have a number of procedurally generated levels belowground with cave like appearances, and each one of these levels acting like separate "worlds" with different appearances based on what Z level you are on (IE Lava lakes in Z -40 and underground lakes/rivers down to Z -39 and ores generated to the locale/Z number of that level.)
*A Skyscraper system which works similarly to the digging system in that you may place elevators/stairs/other entry methods in one floor of your factory that is walled using a separate kind of wall from normal ones (Structural walls?) that requires a closed shape with structural walls/gates that defines that there is a Z level above this, the only difference from the digging system being that you can see the regular world (Z 0) with a depth to represent that you are looking down upon it rather than it appearing flat.
*A mountain system that works exactly like the digging system, with the only difference being that it shows the normal terrain like the skyscraper system, and includes the ability to dig out of the mountain and interact with the world one Z level below where you currently are
*Bridging the gaps in the Z level logistics issue (IE getting an iron ore supply from a mine on level -19 to level 0 for smelting using something akin to the elevator system, all except with something akin to underground belts which utilize a certain length of x or y length to represent a belt angled upward in addition to the Z level climb (say 4 levels/belt) And for logistics bots/other bots you can either: use the mineshaft system or add in a special port for robots to descend/ascend. Same way for vehicles, and aliens.
*Mineshaft depth descent can be configured by clicking on it, and having a +- system for how deep you want to go. Same with the belts which ascend/descend.
As for the lategame resources I think that would not work. I think you should configure it where you have upgrades of mining technology in a single miner like the electric miner, that gets upgraded gradually like the weapons with a +x% for efficcency/speed instead of damage , and certain upgrades that allow you to tap into resources which you couldn't have harvested before, (IE take titanium ore from Bob's mods, and make that require a titanium extraction upgrade be researched but still keep the one miner mines all approach) And I know this sounds a lot like the modules system, but think about it, as time progresses you should theoretically, become better at mining things faster and getting more from a resource node than you did at the beginning if you research it, without the need to manually upgrade things using modules. That being said, it would also complicate things because making something more powerful as you go along makes it consume more energy, which is why I am going to suggest that you implement instead new modules for mining certain late game ores and then a miner module capacity upgrade system instead of hard upgrades, as this allows for a more modular (Pun intended
that was awful for a joke...) approach, and allows for technological innovation as well. I also encourage you to expand the module system further to represent more technological innovation.
However, whatever you decide to do I must ask that you please keep a setting implemented in the world generator for a flat world, like it is now, because some people like that, and various settings for mountains and an enablement/disablement of the z system. This way you hit the largest sales base in addition to making a great game that many people can enjoy, and so in the end, we all get what we're asking for with the Z system.
Thanks for reading, Hope this helps,