I've read a lot of posts on this and just thought I would throw in my two cents.
1- There needs to be a cap on how many mines can be deployed in a system. It should be low, like maybe 10 or 15 at most. If you allow more then that you simply adding too many objects and it's just going to slow the game down too much. This is a really great game and it would suck to see one item get spammed so much that it becomes unplayable on some computers.
2- There needs to be an automated way to clear the mines. In real life you probably wouldn't jump a major fleet into a warzone without doing some recon first so give scouts the ability to detect the mines. This also gives the player a reason to build scouts that travel with the fleet. In addition you could limit their detection radius so that it doesn't see mines throughout the entire gravity well. This gives the player a reason to keep a scout or two with your fleet at all times even as your traveling through a gravity well. To clear the mines you could add a clearing ability to the flak frigates so that the two ships have to work in tandem with each other to clear the mines. This way the mines still function as an impediment, as they were meant to, but it's not ridiculous either.
3- If the above 2 options were implemented then I think you should also increase the penalty for not scouting in advance by making the mines more deadly. In my opinion this is only fair. If you have the ability to send in a scout before your fleet to check the system for mines and you don't, then next time around you'll be certain to do it right. In addition to this I saw someone else post that mines should not discriminate friend or foe and I would have to agree with that. Mines should act like a strategic road block that can buy you some time to move fleets around to defend a system or placed on a key choke point but at the same time not be insurmountable.
I think with some minor adjustments mines could be an excellent strategic and realistic part of the game but in their current state they definitely have serious issues.