Do you think it would be possible through patches and expansions for Stellaris to have an economy more sophisticated than Command and Conqueror? I feel like the game is seriously lacking without one but it also seems like Paradox kinda backed themselves into a corner by having only two resources, a tile based building system and monolithic pops.
I am not convinced it makes sense to try much more detail. For a paradox game, this is already a unprecedented level of detail. Consider that each System would be a Province in EU or CK.
The design was clearly to keep planet management load rather small. Indeed it must be kept so small, the AI can do it. Building up planets is a nice little distaction early game. But late game with all those planets you will conquer it will likely not be that interesting. This is a Grand Strategy/4x Hybrid. Micro-managy stuff and Grand Scale do not mix.
Also note that there are much more then 3 resources with banks:
Food, Energy, Minerals, Unity, Influence, Science (in 3 Flavors).
Adding more resources does not make a game better. There are a few games that have up to 4 resources. They did not become better with that, only more complex. Complexity without Depth* makes a worse game.
Actually even having that many resources that still mater all about the same amount is a feat worthy of praise.
*This video explains it better then I could:
