Have you considered using OverlayFS in a future version of Docker, instead of AUFS? It comes bundled with Ubuntu 12.04 and higher, and my understanding is that it could possibly get merged w/ kernel 3.10
Merging aufs into mainline feels like the logical thing to do, but clearly someone in the chain disagrees. It's disappointing but it is what it is.
Btrfs seems like a more likely alternative for docker.