Filesystem access etc. has to, at some point, cross the barrier from VM to native code. Sure Node.js has file-system access (and other stuff) built in, but willingly moving in a direction that's non-extensible seems odd.

I know you've since said you'll just pull native modules out of the cache, and I'm perfectly happy with that. However, please don't overlook the importance of native interoperability because the code you tend to write abstracts this away from you. Native interoperability is what makes Node.js.