A micro-kernel, with a linux virtualization layer, being abble to run Linux executables as if they were native.
My hunch is that in the long term, Google will probably use Zircon as the 'first-level' kernel, and run the android apps using some emulation layer.
Maybe it could be the answer for what you are trying to accomplish, without having to create a whole micro-kernel OS from scratch, while at the same time benefiting from whats already there.
I bet that with such a thing in place, the Linux kernel could totally go away, with only a emulation layer in place if you want to.