Before I start, I'm just SLF, so anyone in the know please jump in and correct what follows.
I understand that a lot of the cost comes in because all of these bits of paper need to be manually reconciled for inter and intra airline billing and paying the travel agents who issued the tickets. e.g. code shares, tickets boght in one country and changed in another where a supplement is paid, checking used legs against paid legs, refunds for part used tickets all need to be netted off.
Obvioulsy if it were all eletronic and on compatible systems this would be able to get less costly, but getting there will cost a lot, and at the end of the day passengers like tangible proof of thier imminent travel as opposed to a locator number.
At one point Swiss air were flying all the ticket stubs to an Indian IT company for entry into the reconcilliation system in order to reduce labour costs, not sure if they still do - perhaps others have followed suit?
You might find some details of the systems here :
http://www.iata.org/idfs/settlement.htm
I've not read it, it did not look that gripping!