The AI... doesn't respond to mine fields. It will happily plow through a field of mines if that is the shortest path to its target. Usually you sidestep this with a series of shift commands. I.e. "move here first, stupid, then turn and bomb the planet." Enabling a fleet while in that gravity well and assigning a series of orders to the flagship will ensure that all over ships don't have much opportunity to meander about and into a mine field.
Scouts generally target mines first, since they have the ability to decloak them. But on their own scouts take a long time to clear mines, even if you have 10 to 20 of them working on it. The scripting for revealing mines isn't tweaked to differentiate when one scout is already targeting a mine. This means all 20 might go for the same mine, then all stall out once the first one gets there, only to repeat the process for each mine. To prevent this you have to manually spread them around the mine field so they can begin 'eating' it from the edges.
The developers mentioned bringing flak along and assigning to a mini-fleet with a scout as the flagship to force mine clearing duties(set to tight cohesion for best results). But auto-join fleet behaviors are turned on by default for many ships, and this can cause its own headache. I'd have programmed a flag that would allow you to select whether or not ships could auto-join an existing fleet. Call it CanJoinFleet or something, and put a putting on the fleet management tab. That way you can turn it on or off to override the auto-join fleet behavior without wasting micro time on all of the ships that you make. Then if you want to add more scouts or flak you can still do it manually, since only the auto-join behavior would look at the CanJoinFleet variable. The scout/flak mini-fleet is still good a mop up though, say when you have a siege frigate finishing off a planet and your main force in the area has moved on.
I laughed when you explained the shift key 
So what I thought was right, if there is a minefield and the desolator just start bombing a planet, it will move towards the planet automatically, stupidely go through the mines, deploy the platform (eventually in the mines) and continue if it's still in one piece (doubtful) so micro-managing is still very important at that point (I guess Starcraft and C&C didn't teach me well AKA build 3000 tank, BLITZKRIEEEEEEG !!! ooh I won ! And who cares if there were some casualties?)
Ya, I noticed for the scouts, but it's not always easy because you would have to send the scout before or after or in the middle of the battle, before is a problem since there's 103.4% chance that the scout will be destroyed by other ships, platforms, defence and whatever can make him go boom.
Then you can send it after, but then again your stupid fleet might just start harvesting mines (it's the season, they're in full bloom and they look so ripe, how can you resist to pick one? 
[e digicons]:karma:[/e] ) while trying to move towards platforms and other ships.
Finally, you can send your scout in the middle of the fight, which is probably the most effective way to do it but you'll probably go crazy to micro-manage the battle, the skills of your capital ship(s), preventing your fleet going in the minefield and your scouts to destroy the mines... 
Well, I just love mines but fighting against them is really hellish 
The mini-fleet can just be destroyed if there's a fleet stationning in the planet so it could end being a waste too, isn't it? Your mod Idea though, sounds totally great for that case
