I ponder the same question late at night sometimes... We are adding options into the powerstore in the next release.
It will use separate products in the products table for each possible option combination... this way you can have separate inventory, sku, description, or whetever else you want on an product by product basis.
We add a checkbox to the update page to "update all options" in the case that they want a single SKU across multiple combinations they can quickly update the description, size, sku, or inventory of all of the items individually.
It ended up requiring some pretty complex querying and functionality to pull off on the back end and make easy to use at the same time as providing the functionality needed.
The hybrid approach may be good as you suggest but it would add complexity on something that is already pretty complex. I don't want to say it is a bad idea, since I have pondered how to create a store that works well for inventoried items but doesn't have all the complexity for uninventoried and a hybrid approach may be necessary in the long run to accommodate everyone's needs.
