Absolute customisation: Build infinite choices for model & versions! Set rates for fixed / percentage options, 12 types of options, sku rules, regular options, stock options.
Conditional Logic: Put adjustable dependency on the commodity choices - show/hide options depending on what the customers want.
Pictures & swatches option: Add photos to the product choices. Using image/color/text swatches to display choices for variations at its best. Replace an picture of the commodity.