You're talking about converting all auto attack damage to magic damage, then scaling their bonus damage on AP, rather than AD. In essence this is already true for the champions that have an on-hit modifier that scales on AP (Teemo, Kayle, Kog, etc.) This is also true, at least for burst, of Poppy and Twisted Fate, the latter has a minor scaling AP on hit, as well as a magic damage converter for his auto attack in Pick A Card (It should be noted that this skill was, and probably still is buggy, and didn't properly convert lich bane when it was physical).
Additionally, those on-hit damage modifiers have their own base damage and additional effects, which makes them even stronger.
Still, an AP carry that was focused on auto attacks is feasible now, and is a design I'd like to see happen, preferably with something to emulate critical strikes like TF's stacked deck does.