So I read in the latest dev journal how the team decided to move the resources away from individual locations to a global pool.
I'm quite sure that this is not a bad idea, but I still wonder if it's not possible to somehow retain the ability to keep these resources actually located on the map such that you (as an enemy) can interact with them.
The new space4x Distant Worlds has taken automation to an extreme, and I would not suggest that elemental needs to move in that direction, however, the resource distribution model in DW would seem to be one which could also work in Elemental.
That is that while you may be the ruler of your empire, there is also a private sector which will take some actions independantly of your direct control. In Elemental as it pertains to resources this would be limited to merchants who automatically generate caravans to move resources around your empire. I would suggest that you are allowed to set priorities at different cities for how much or which kind of resources are taken there, but otherwise the process would be seemless, other than you seeing your merchants sending caravans around your empire moving the materials to where they are needed/desired. This allows for some additional strategic decisions if you feel the need to devote some amount of your militray to escort the caravans, or to clear out your countryside of various NPC type threats before you plop your pioneer on that gold mine. It gives attackers the ability to capture or destroy or deny resources in more ways than simply by taking the resource site.
The other aspect this covers, is to make your empire look more 'alive' or 'organic'.