Product attribute/option logic
I know that this is probably way beyond the scope of what you're planning but it would be nice to have attribute/option logic. For example, when buying a shirt the colour blue is only available in large but tha same shirt in red is available in large, medium, and small.
For me, aside from the needed UI/Admiunistration work, this is the final step in making product attributes/options near perfect. The only thing left after this would be to do kits :)
Having said that, I still don't fully understand how products will work in the future but I guess that will come in time.