Idea on how to "fix" the mining system: have it scan planetwide on default, but not detect anything. Then, as you scan a more precise area the sensitivity of the mining sensor goes up until you can clearly make out the exact location of the ressources and send a probe. Makes it less "combing the planet" and slightly more of a puzzle.
As for combat... have defensive and offensive abilities on different cooldowns. Defensive abilities being shield bonuses, pull/singularity powers and ammo powers, and offensive abilities being anything used to deal damage.