Oh, targeting a good VM is a huge win over a typical machine language for an implementer. My prediction is specifically that the inter-language paradise some expect will never come.

But even within the points you bring up, I'm not sure that VMs are as winning as they're made out to be. Size and compilation time aren't somehow intrinsically better for VMs; JS does quite well on both fronts these days. And I'm not convinced JS's quirks are harder for implementers to cope with than a silicon machine language's.