Ok, I understand just what you are saying, and this is exactly how PowerStore works. I will give an example for this.
I have shirtX, first I add this item in the admin back end. Once it has been added I will then add options. The first set of options that I would like to add is size. I create this option, then I create values.
Next I create the color option, then add choices for this. Once that is done I go to manage options, in here I select all of the available sizes for the colors and add them to the Available Online column.
Once they are all available next you update the product again. Now you will select your first size and color combination that will have a price that is different than the default price you set for the item. For example I will make it so if you select small, then the color blue the price of the item should be 12.88 instead of 10. With the size selected as small, and the color selected as blue I just go down to the price field and set it to 12.88, I also make sure to add the inventory amount or click the checkbox for unlimited inventory.
Once you do this you can go to the front end, select that item and view it's details. By default the item is 10, but if I select a size of small, then select blue as the color the price is updated to 12.88.
So from the perspective of the admin and the user on the front end there is only a single product with multiple product options. Any combination of the options can alter the price of the item.