The solution I found to the problem with aircraft was to change the AI behaviors. In the fh2/ai folder, there's a file called "aibehaviors", or something like that, that handles how AIs behave in response to vehicles and such. What I did was turn their "move to" weight for fighters and bombers down to zero. The default is like 7.5, which means that if they see an empty plane, they will almost without failing try to get in it. At 0.0, they don't try to get in them very often at all, and if they do get in the planes, they either idle on the runway or fly off the map and die.
But I agree that, while it is more interesting to have the bots use the planes, they are so overpowered that no matter what I try to do, I die instantly. One solution, however, without changing the files is to simply hop out when the stuka is on apporach; they wont bomb you unless you're in a vehicle.