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This example t-shirt includes both color and size selection. Editing it and browsing to the attributes, options, and adjustments tabs will demonstrate how Ubercart handles product variations as opposed to e-C's subproducts system. Custom development must include a tab that displays a table of checkboxes where you can disable certain combinations. The add to cart form can also be modified to function like the existing form that allows you to add products of a multiple size to the cart at once.
Furthermore, as you can see, by default attributes can only have a single flat rate increase/decrease assigned to them. This means the difference between an XL and an XXL shirt cannot depend on the color, but right now there is a color-dependent difference in your store. This would require some customization as well, and certainly a little bit of brain work to figure out how to best achieve a UI for it all.
It is possible to update the prices dynamically and change the option displays, so don't sweat the weird look of having the +whatever in the select box.