Scheme flags an error on car/cdr of nil. Common lisp doesn't. Now you're suggesting doing this for all atoms. I like this because it loosens another constraint I hadn't even noticed. (http://arclanguage.org/item?id=13414)
I think in the end just extending car/cdr to support atoms would still be useful, but changing lists to being nil terminated only some of the time would likely be too inconsistent and/or buggy to risk. It would save some space, but on the whole doesn't really improve much.