How to change the order of attributes in the Ubertcart cart page
By looking at ubdercart's theme_uc_attribute_add_to_cart function and how it is themeing the output including attributes, it appears that you can achieve what you want by implementing hook_form_alter. I would start by finding the form_id, perhaps by adding a debug statement in the function. Then I would implement hook_form_alter and would alter the way the attributes are ordered to my desired order.
If this does do what you want, try and follow the logic to see where the attributes are being themed and/or built. Then hook into that mechanism (form_alter or a preprocess function) and  I am confident you will achieve what you want. 
Hope this helps.