I'd love the following:
1. All factions get a tech where their fighters can detect mines and take them out. You have to research this of course.
2. You can toggle mine clearing on the the host of the fighters like toggling auto scout or auto drop sensor drones.
3. Fighters whose host has auto mine clear turned on will clear mines, assuming no other hostile enemy ships are in the well.
Thus after you take a well you can build a hangar or just have a Perechon hang around for awhile as the fighters clear.
I really feel the game would be a lot more enjoyable if mine clearing was passed off to the AI. In real life we're already making mine clearing drones (BAe's Archerfish as an example). It seems reasonable enough to assume my techs could come up with something my fighters could launch to clear the mines, while the fighters remain at a safe distance.
Or since we already have militia techs for the Terrans, some tech to allow local defense force crews to board the constructors and autoclear mines if they have no other orders. Basically what Zaydin said.
It's bad enough my fleet commanders can't even execute a jump or move into proper fighting formation with me babysitting them,but the fact my system defense commanders can't even autoclear some mines makes me wonder how my people ever made it into space.