How would that make it impossible?
Mathematically, 5 million people will out breed two. Even if the 5 million are borderline retarded, if they were successful enough to breed up to 5 million, they will continue to breed.
You make these claims, but you never provide examples. Why can't the Lord have spread the children of A and E to the various populations? Why can't lines that ultimately don't result in mating with a child of A&E die out? What if, for example, the Flood is a metaphor for that? There are just too many possibilities.
Examples? Tasmanians, for one. They walked onto the island, but the sea flooded back after some ice melted and they were isolated.
http://en.wikipedia.org/wiki/Tasmania#Indigenous_people Furthermore, before you put A/E-ites in a boat to Tasmania, remember that they also never "progressed" beyond the technology levels of the Ej Meh-ites, so by your own measure the indigenous peoples are inferior. Yes, inferior humans.
The FACT, and I mean science here, is that Ej Meh-ites are equally as intelligent in every way as we are. Why? They are us! If you want to say god waved his magic wand to hide this or extinct that, then you have rejected science. Your hypothesis contradicts science, it contradicts math, it just doesn't work.