Simple and sweet.
The scout ships had problems finding the mines and then seemed to be inexplicably killed by the mines
Mines killed more of my ships than the enemy fleets
Mines were spammed all over my systems by my allies. When these allies turned I was stuck with lots of stupid mines in my system, which I could not kill while they were my allies. Lots of fun clearing out hundreds of mines left behind when my previous ally "helped" dropping mines in my system.
So here is my proposal about what I would like to see.
1) Scout ships have an ability to detonate mines automatically. Let it cost 5 or 10 antimatter with a cooldown of 5-10 seconds. The scout ships automatically go to the nearest mine and detonate and work their way through the mines through the system. The scout ships would also be invulnerable to mines.
2) Mines are automatically targetable and can be destroyed if the player owns the system. If need be put a structure or ability in the tech tree to give this ability to the player. This prevents players from spamming a system and then waiting for the alliance to fail. Defense platforms should be able to locate and destroy mines.
3) Ships do not automatically fly through the mines to attack other ships. It is very annoying to see your capital ship constantly attack your opponent and be destroyed because it flew through all the mines.
4) If there are mine limits in the future make it so players can set an area to place mines. IE mine fields rather than as many mines as can fit in a system. Make it a tech tree option for a player so they can have 2-8 mine fields per system.
5) I would like to see different upgrades for mines from anything such as antimatter drain, ability disable, shield jump disable to, homing mines, damage, etc. If need be make it like the starbases where minefields can have different abilities depending on how much you spend (of course reduce the cost to say 400 credits or something). MInefields can be freely recharged when a minelayer comes into the system or over time.