My first idea is: have a system that displays how many members/prime members are in front of you and have a rough estimate of how long their job is. This would allow more feed back to the customer of how long the wait for their job would be and give more peace of mind.
Idea two: Have a table for after you upload your design that would give you the price for the material and cutting. I placed my first order a few days ago and did not like the fact that i had to look through all of the different materials to actually get an idea of pricing. This would optimize the speed in which a order must be placed and also allow customers to receive more information about their own design.
Also, this may not be possible through Ponoko but, some type of plugin for Inkscape or whatever program a customer uses that could give you the price for your project as you go along building it would be helpful.