I like mines as a strategic element also. The AI just jumps around them, though, so they don't do much good unless you surround the whole system, which is insane expensive. I started to just build them when the bad guys jump in, or surround my facilities.
Maybe best solution is that every time you buy mines they go around the whole system and subsequent buys are more expensive but make the field denser.
I think the homing mines are way unbalanced. In the game I'm playing now, the bad guys dumped a huge swarm of them in a contested system and there were proximity mines left over from the previous owner. I took a fleet with 15 capitol ships all level 8+ and destroyed the colony and facilities. I was going to take a fleet of scout frigates in as chum to take out the mines, so I started to move my fleet out of the system. When I turned around, a ship swung into range of the homing mines and they hunted down and killed 3 of my best capitol ships after I had just wiped out all enemy opposition.
My suggestion would to allow flak weapons to take out minefields, or have a specialty minesweeper. Maybe add the ability to a ship via the tech tree. Or allow everyone homing mines (maybe via the defense tech tree).