Hey, SJ, you're a General now!
As for mines... You don't need an obscene number of them everywhere, just at strategic locations. IE, for the problem of the 250 system empire, that means there are a max of 5 systems for enemies to be in (hardcode limit of 255 systems because of char array). That means that you will only really have to have mines a few systems in from those five, and over important planets. Not to mention that if you have all your enemies down to five systems, you could easily send in a "small" fleet for your empire to swat them out of existance
For the mine size... if you have mines early and enemy ships are around LC size, then small mines are ok. If you can't fill up a sector with large mines, but can with small, use small. If your enemies have enough minesweepers to clear a full sector, screw the mines, build fighters for warp defense (depending on weapon strength, Groups of 10-25 put into a fleet work nicely). Satellites can work too, but they'd be in one big group, and can only fire at one ship at a time, and can't move (which sucks if you end up at the opposite end of the warp and can't get some point-blank shots in).