A great fucking way to get minerals and shit is salvaging from a battle. Have a space battle, or maybe an assault mission and then you just recover items. The harder the mission, the better the payoff.
The problem is with space battles in the ME universe. If you read the codex crap from ME1 they say that it's basically huge capital ships in a battle of attrition. Fighters are basically suicide attacks because automatic targeting vaporizes them
Then let's go pirate and have it be more of a scavanging operation. You find a derelict vessle, have to traverse it's creepy hallways, and pinpoint locations where minerals can be extracted. Some of them contain aliens, renegades, or volitile conditions.
That's a damn fine idea. Taking that a step further with a renegade twist...raiding and boarding ships that aren't abandoned!