I think you might of hit it there. Instead of allowing one resource per ship per mine. You could have a limited number of resources per resources. Mining either one resource per turn, or a number of turns. This still doesn't negate my idea of having all buildings, ships, and technologies require resources.
The closest thing i can think of that would work well with your idea is to have resource 'pools'.
So resources are mined and build up over time just like money. Then you spend various amounts whenever you build something, and also a very very small portion constantly required for maintenance.
Whenever you get low on a particular resource, you might not have enough to construct that building or ship you want. And if your maintenance eventually gets too high, it becomes a problem too, just like it can now with money.
This will all generate a great deal of interesting strategic challenges and is far more realistic than the current model.....
Oh and yes, anomalies wont be forced to grand permanent resource bonuses - that's just so weird, it will be able to do a one off addition to the resource pool instead.
Edit: I got this idea from a very old game 'Total Annihilation' which operates with metal and energy pools.
Another idea from that game is the special metal making buildings that convert energy to metal.
Then what you could do in the game, you could have finite resources, that eventually run dry. Then you have to rely on resource creation structures that make each resource, but its expensive, and produces very little, since its a rare resource, and very difficult to reproduce.
Or you could go the way of Starcraft or warcraft.... once the gas or gold on the map is used up, its used up, the end.