I have just hit this glaring omission from the woocommerce e-commerce plugin as well. I can't believe the absence of a system that automatically calculates product variations and the their prices.
I have set up a shop where each product has the 3 options, each with 10 sub-options. So that i have to manually calculate the the price variation for 300 combinations, for 20+ products.
This should be done automatically, i am coming from PrestaShop which does this automatically.