I agree that there should be another way other than the mysterious benefactor and level up bonuses to get things like Flight Certs. Maybe one could be able to buy it with the in game cash (albeit an obscene amount, probably, but that's understandable.)?
Repair time definitely could be reduced a fair bit, or have the repair points for each plane go up quite a bit. I'm enjoying the game, but it does put a damper on the fun when I'm in the middle of a quest and I need to wait so my plane is repaired.