I have everything turned on with two exceptions: aircraft overstress and collisions with other aircraft.
Overstress was turned off after I was flying along on a long (LA-Hawaii) flight, and the wind suddenly shifted. Suddenly, my normal .82 mach speed was bumped up to .93 mach. The autothrottles faithfully decreased right away to compensate, but could not get the speed back to below the .86 max mach number before the plane overstressed and crashed. Seeing as those kinds of incidents are the only times I ever get into overspeed or overstress, I just leave it turned off, and protect my hair.
Collisions with aircraft were turned off for protection from idiots in multiplayer, but I'm too lazy to switch them back and forth, so they stay off. I can trust myself not to hit any AI
traffic or anything.