dolittle, I think you raise a fairly common issue for "combination sale" shops, but I don't think the solution is to change the attribute system. By very definition, the word "attribute" seems to describe a particular value or component on the product, not choosing other products from the catalog to add to a product. While attributes can be used to specify component parts of a whole, attributes should not turn into the way to allow customers to build a custom product kit (which is essentially what you're describing). There are other options that make more sense.

The main one is that of a new understanding of product relationships. Products right now may be stand alone or grouped to be sold together together in a kit by the administrator. There is nothing that lets someone piecemeal create a kit and add it to the cart or choose an add-on from the product catalog. We've tossed around the idea of accessories in the past, and that seems to be more like what you're describing. There's one core product (a computer system), and then the customer can choose to add a bunch of related products as accessories (LCD monitor instead of a CRT, wireless keyboard/mouse, etc.). This would have to start as a new module and perhaps build its way into core. It would take some work to figure out the best UI from the admin and customer sides.