While a full database system allowing for relational databases would be nice, I can live with the current setup. However, the ability to write custom queries would be a huge addition for us.
We currently have 4k+ products and have another 6-10k to put up, depending on how crazy we want to go. The ability to create links that return customized product lists is very important to us. We need to be able to list price ranges, features, etc. in a link, and have the database return a page that's not been already created as .html. I guess what I'm asking for is some ability to create dynamic content pages based on our product information.