I fail to see how booking in advance would really help the OP because he's presumably going to end up waiting in a line no matter what (there are plans to upgrade the eticket machines to spit out pre-paid tickets based on passport scans, but I'm not holding my breath to see this arrangement any time soon).

The OP's goals are presumably to: 1) minimize his time at Hongqiao; and 2) not miss his train.

Given the uncertainty of the airplane's arrival time, a conservative approach to #2 would necessitate a 2.5 hour cushion even though he could probably pull off the entire drill in around an hour.

Unless he is traveling at a particularly busy time, I'd be inclined to roll the dice and buy tickets at the station. That route has a staggering amount of supply.