My tactic for clearing mines goes like this: First, before sending in a fleet, send one scout (or whatever is avalible) in to the enemy system, to see where they have grouped thier mines (AI usaly only builds mines on one side or or right on the phase line), this also causes the AI to move any ships it has in system to that area my ship jumped in. Then I move my fleet (still in my system) to the oppisite side of the phase line of the mines and out side of the grav well before ordering a phase jump. Before I jump my fleet I order all my strike craft to dock, this helps alot with keeping the ships together when they jump (even with the grouped jump, some ships dont right away, because thier fighers are still not docked and delays them from jumpping with the rest of the fleet) Then I jump them, and they usealy (sometimes not) jump in the enemy system away from the mines. (Dont forget to undock your strike craft). With practice, you can get pertty good at jumping them in so the formation is facing the enemy ships. I will attack any starbases first, with all my ships and bombers (I let the fighers attack any enemy strike craft), then worry about the ships. Then after I take out the enemy planet, I send 3 or 4 scouts into the mine fields and let the fighters take 'em out, as my fleet stays in that system for any counter-attacks that might happen wile Im building my new planet up. This is a late game tactic to use with large fleets and vast resorces.
For Early to mid game just build 3 or 4 scouts, then 2 light carriers and send them in (dont fleet these ships, it will cause the carriers to move in to the gravity well with the scouts, and into the mine field) Keeping your carriers out of the grav field, send your scouts and strike craft to detect and distory the mines (you may have to manualy control the strike craft to attack the mines as they will try to attack other things in the system first). If there are a large amount of enemy ships and or a starbase in range, get your ships out right away, cause they probaly will be distroyed before they can clear any mines, you will have to use the above tactic to crack the system defences.