They did try this when they made the Mordekaiser juggernaut update. They did their best to balance it out but it was always Overpowered or underpowered (judging from the fact I haven't seen a morde bot in some time). It's possible the problem was they were trying to do this with a tanky melee character instead, but I do think this is a cool idea. It is possible to do a bot lane with two AP champs based on whatever wombo-combo things you can think of like but I think this would add alot of variety.
As Atinizer points out, this could force ADC's to get a maw or mercurial first item, but I don't think so. It's not like they build Armour when they're laning against an ADC and an AD Support. ADC's are supposed to be squishy but focus on dealing damage with their support worrying about how to keep them alive. I guess there is Corki and whatever, but more potential AP champs bot would be cool and great for team comps that already have 3 AD champs in jungle, mid, and top.
There's also things like AP Kog'maw or AP Miss Fortune you could mention but neither of them are really "Meta" and you're usually sacrificing the huge amount of single target damage the AD builds give. AP MF has some mean AoE damage but again, a character thats like Sol from SMITE, specifically designed to go botlane with a support would be great.