Part of the problem is that the handling agents don't have people with the right management ability to deliver what is required. Because the lo-cos have primarily gone into regional airports, the agents there have gone from one flight a month to perhaps 60+ movements a day. Most of the management are people who have gradually moved up the organisation from within, or moved across from a fairly junior role elsewhere at another regional airport. they just haven't got the experience to deal with the increase in pace and complexity.
Sure, most of the equipment is old and knackered, but issues like training, scheduling and communication are all within the control of the management at very little or no expense. This is where the operation inevitably falls down, and because managers don't want to hear about constant problems in these areas they lock themselves away in the office. They're OK, earning nice little bonuses fiddling departure times and delay codes so why worry?
Replace them with some decent managers who are going to be held accountable for their station's performance (including an element of customer satisfaction), and things would improve for everybody. Staff would be trained and able to do their job properly, people would be available when they were needed rather than when some dizzy so-and-so decides to put them in a schedule, and everybody would be kept in the picture with regard to the operation so problems can be dealt with as they arise, rather than when it costs a lost contract.