Staffing for small airlines/small planes has already been tuned once or twice, but seems they still aren't good...
The suggestion about having staff (or at least some of the groups) calculated based on the number of passengers/seats offered would help. for example, if you fly planes that only carry a few people, you don't need an army of customer service or safety&security people.
Also, I think that it would be good if a small company could buy the maintenance services from another company (player- or computer- driven) so that they don't have to pay huge salaries to maintenance staff to have a couple of A checks done every second evening (thus, maintenance needed 30h/week= 30h from 7*24=168h is 17,8%. So, the maintenance staff is sitting 82% of the day doing nothing (apart from B and C checks)).
This would already help a lot, since at least for me, customer service and maintenance staff groups are the biggest after pilots and cabin crew.