I would like to see a product customization solution 2.0 with backreferencing-entities like profile2.
Commerce Product Option does it this way but it seems dead in terms of maintainance and it seems to use ugly hacks for the add-to-cart form.

This approach would offer some benefits:
* define option bundles like "common options" and "product x options"
* define which option bundle to use as late as in the add-to-cart form

(I see this as an architecture issue for the commerce framework so this maybe should live in the commerce project.)