Disclaimer: I will not present a perfectly balanced idea, so don't nit pick on the details, this is all about concept.
In general: Mines would become an area of effect damage over time that has a chance to do substantial damage instead of a constant rate of damage.
Mine fields should be a very risky thing to navigate. To save processing power, Minefields would be an area of spherical space instead of individually drawn mines. Some colorful dots at a distance would be seen for minefields that aren't cloaked enough to know that they are there, but when you zoom in very close there wouldn't be anything. Mine fields are "too small to see" when compared to the size of planets.
Once a mine field is built, it can be replenished in various ways that won't need another infusion of resources, or at least a smaller cost of resources. The terran minefield would be replenished via a new structure. The advent and vasari mine laying vessels would have a "replenish" option that would cost less or nothing at all that could be set to autocast. The vasari minelayer would use antimatter for this ability and have a long cooldown, the advent would cost production time and antimatter at the drone hosts for the minelaying ships, and then would cost the ships themselves as normal.
Mine fields that have a % chance to kill/damage a ship that remains inside of them for X amount of time. In essence a minefield would be a "zone of death and chance" that could be navigated successfully if you are lucky, or you could lose a large part of your fleet if you are very unlucky. This danger would deter most players and would provide an effective defense. Naturally each race would have different overall chance of killing ships in their minefield. the Terrans would have the most likely chance to kill an enemy fleet, followed by the Vasari and the Advent.
A minefields Hit points would be the amount of mines that it has. A scout would fire once and kill a mine. Mines would attack ships inside of them at X amount of mines per second depending upon the total amount of mines avaliable. Every mine lost reduces the chance an enemy/friend will be hurt by the minefield, until at last the minefield has expired when the last mine is used. Every mine in the mine field would be a % chance of hurting an enemy ship, and the amount of damage done would be a % chance as well.
ALSO, an important addition, an enemy wouldn't know how many mines you actually have in the minefield, so even a minefield with one mine in it could deter an enemy moving through it. The only way to find the number of mines a minefield has would be to send a scout next to it and start attacking it.
For example:
Say a mine field has 100/100 mines in it. Ship A comes in and starts getting hurt at 100% mines per second. Ship A gets destroyed quickly, taking say 5 mines (or chances) with it. So now the mine field is at 90%. Ship B comes in and starts getting hurt by the minefield at 90% of the maximum mines per second. Ship B ends up taking 10 mines with it. Ship C enters, and takes a mine attack from the minefield and takes it at 80%...so on and so forth.
The numbers can be tweaked to optimise memory use and it could be simplified that a minefield would go down at a rate similar to the logistics slots of the ships destroyed in it.
So a minefield at full strength would be dangerous, a minefield that has had a fleet pass through it and detonated half its mines would be half as effective.
Mine fields are a two way street for the vasari and terrans, they hurt your own ships as well as the enemy. Advent have mines that can better home in and recognize friend from foe, with the lowest payload and area of effect of the three species.
For convenience trade ships wouldn't be affected at all by minefields, I would foresee it causing too many problems, mainly you would stab yourself in the back.
But if the developers want to make a new kind of economic warfare, be my guest! 
Offensive use of mines by Advent and Vasari:
Both races would have their minelayers/fighters create a zone of death that is smaller than the terran's huge planetary defensive minefield. If a terran starbase gets an offensive minefield, it would be larger than the vasari minefield(more on this later).
For Vasari:
The vasari ruiners should be slower and turn slower. The Vasari minefield would be medium in size and cost relatively similar to what it already costs and do similar damage. Vasari minefields would also harm their own ships inside of them, this includes the upgraded gravity mines. Vasari mines should take the most care to properly use as the vasari subverter/mine layer combo is very strong. When using an antorak marauder's speed increase the vasari mine layer speeds should be what they are now, and any gravity minefields would be negated by the ability so the vasari fleet could escape.
For Advent:
Advent mine fields would be the smallest in size and overall fleet damage, would home in on enemy ships at a greater range and wouldn't damage their own fleets. The Advent homing minefield act normally and are the only mines that don't damage friendly units while in the area. Scouts would counter this mine field and be the only ship that isn't targeted by them. The smaller size of the mine field would make it more difficult to push an enemy fleet into it with guardians.
For TEC:
TEC could build a mine field structure that would be visible(depending upon how balanced it would be) yet the mines themselves would be invisible. The mine laying structure would have a designated area around the structure (similar to the radius of a repair bay, or whatever is balanced) that would cloak all mines. The structure could be destroyed safely with strike craft and scouts would also be a counter for this type of minefield. This would alert players that the planet indeed does have mines, but it wouldn't let them know the EXACT location of these minefields for safe navigation. Terran space would be tricky to navigate. Scouts wouldn't be able to detect the mines UNTIL the mine laying station is destroyed. There would be one minefield allowed per structure, or whatever number of mine fields makes the most sense!
The advantages of these Ideas:
Less CPU needed to draw the mines
Ways to decrease costs once a minefield is built, and a way to replenish minefields easily.
Easier balancing, mine damage is now chance based and ranges from a one hit kill to no damage per second. As long as these chances are substantial enough, the mine fields will be a significant deterrent worth the value of the research put into them.
Disadvantages:
lets see what someone in these forums comes up with .
Some other minefield ideas aside from the others stated above:
1. I think that the TEC need a reasonable offensive ability in their starbase arsenal. I would venture that a freshly built TEC starbase have the option to deploy a smaller, balanced minefield in an enemy gravity well to assist the TEC fleet. The vasari starbase gets movement, the advent starbase gets fighters, and the terran starbase needs an advantage as well. It should get a smaller than normal minefield that does less damage than a normal TEC minefield, but that does do more damage than a vasari or advent minefield. A TEC player could place this minefield anywhere inside the gravity well, or within a certain range of the starbase, whichever is balanced.
2. Give one of the sucky advent capital ships a mine laying ability just for kicks (just antimatter cost, no credits) perhaps it might make one of them useful. Or the developers could give halcyon's/advent starbases the ability to make mine squadrons as well.
3. Give TEC and Advent a mine upgrade specialized to their race similar to what the vasari have. An advent minefield could be upgraded to reduce the antimatter of all ships inside of it by a balanced amount. TEC should have Fleet stunning mines as an upgrade. The "stun" will affect each ship once upon entering the minefield and would completely stop the ship reducing its speed to zero. This would mean that ships caught in the minefield would stay in it longer and would take more damage from it making it an even nastier surprise.
