Leave the fog as it is, and fix the cheaters. Flying high above the fog is relatively clear, and if you see too much fog you had better pull up. Really though, I want the dynamic weather effects. That's the ultimate solution to the issue.
I think the cert gain is fine the way it is, and I honestly like the prices. If anything I'd make the certs have more of an impact once unlocked, which I understand they are already working on. 96 for an RDS persuaded me into certing an AMS Sundy and Spawn beacons instead, which varies game play even more. The price to get your army to battle should be cheap, but having them show up well-equipped should be expensive, as it is now. Besides, I don't understand how people aren't earning certs quickly, the XP flows freely when you're in a good battle.
I don't really have any comment on the home continents issue, beyond a vague fear that I'll be fighting over the same territory constantly. That already happens (less so on Esamir) so there's really no net loss if it happens changed with home continents.