Most importantly the human fatigue. There have been some very alarming reports about regional airlines requiring their flight crew to work very long hours and scheduling them such that it's nearly impossible for them to get a proper night of sleep between working days. They're remaining compliant with the regulation, but in general getting as close as they can to violating. The major airlines, on the other hand, tend to have a more senior and thus more demanding flight crew (in terms of work life balance) so most flight crew have significantly more generous schedules.