The accounting for the paper tickets has to happen manually on the back end. I believe there are a lot of issues related to the accounting of tickets (i.e., while they collect cash up front for a ticket, a ticket cannot be booked as revenue until it is used or voided), so being able to do this electronically is a lot cheaper for the company.

With that said, CO goes through great lenghts to keep everyone on accurate e-tickets. CO tends to do so, even if it means waiting around at the gate, using the GA's time, the Helpdesk's time, all while the customer is waiting. The irony is that it probably costs them more money this way during irregular ops (and it adds to customer frustration since the rebooking queues take longer).

Other carriers can simply associate flight coupons to new flights, even if they don't match. This gets the customer going right away, they still maintain electronic accounting (though it's not as precise).

The point is that etickets don't have to be so painful. CO just makes them a good bit worse then they have to be.