I have a few ideas about the mine problem
First, lower the max amount of mines allowed in a gavity well (to about 50 or so). Now you have to be more stratigic in the placing of mines. (such as sending a ship between gravity wells to see where exactly it jumps in, then placing mines there) This will also help with performence issues, expcaly later in the game when 10s of thousands of mines could exsist. (also no more "structure compleate" after each time a single mine is implaced, please)
Also, I like the idea of a specilized Mine unit. You could call it a engineer unit that can both install mines and dissasimble enemy mines. Dissasimbly would take about the same time as intalling them. make it hard to kill, but have very little attacking power. with this unit, take away the planets ablity to install mines and give the mine ablilty only to these engineer units. You could keep some in your fleets or a few in your worlds for mine field install and upkeep. They could have other abilties as well that might help your fleets out.
Also with less mines in each gravity well, make the mines "magnetic" within a set destance so that a less dense mine field is still effective. You could make the magnetic mine a upgrade for regular mines that you have to reserch. After it is reserched, all of your mines would automaticly become magnetic.
Just a few ideas