Hmm, you could avoid some downloads by basically populating the browser cache by default with some common libraries, like jQuery, and maybe a Lua VM if that catches on, yeah. But this would be totally different from shipping a nonstandard VM, since there is no violation of the standards process if you are basically just optimizing away first downloads of common JS libraries. It does have the cost of increasing the initial browser download though, which is perhaps why this isn't already done (also things like jQuery have many versions which makes things harder).
Note however that Google has not actually shipped NaCl or Dart. (NaCl technically ships in Chrome, but is disabled on the web by default, it is only usable in the Chrome Store.) So currently no browser is shipping a new nonstandard VM - which is good, because if a major browser did that it could fragment the web.