I think the shopping cart is very robust, and the designers did a fantastic job.  Having said that, there are a few things I would recommend for a future release:

1.  The ability to put items on sale in each category at certain times during the year (being able to pick the dates these items go on and off sale).  This would be great for all types of business & for seasonal products, or products you just want to reduce inventory on

2.  Have each option group have the ability to place a picture of the option next to the text listing.  For example, you are selling bicycles with different options for the tires, handlebars, etc.  It would be great to show pictures of the options next to the option itself.  Or at least have a hyperlink with a pop up window that appears right next to each group of options.

3.  If a customer picks one set of options, it would be great for it to automatically gray out (make it non-selectable) another option that conflicts with it.  I know this is available as an addon to BTO, but it would be a nice feature for everyone that sells items with different sets of options.

I will probably have some more in the future, and would love to hear any comments from other users.