I'm most partial to the idea of having a system similar to Dawn of War.
Capturing Tactical Points, Critical Locations, and such for resources; and building power plants for energy.
Plus the Covenant would need something to produce the gases that Grunts breathe.
That way it would resemble having to capture mines that are already there.
And the mine would be set up with some kind of automated mining equipment so you wouldn't have to use any of your personnel to gather resources.
Mind you, I like being able to produce Psychotic amounts of troops and vehicles, like in Act of War and the C&C games, I'm not keen on population limits.
But I'm getting used to having limitted troops with Dawn of War, I still don't like it, but I can deal with it.
Maybe if the resource system was set up like Act of War, where you would have to build a facility on an oil well, or a mine, and have designated "tankers" bringing resources to your supply depot, and you're able to capture, and have to hold, specific buildings, like banks or abandoned supply posts, for resources, being able to capture enemy troops for additional funding/intelligence would be cool as well.
Later..