There is a pretty epic thread that I suggest you just read the tail end of https://github.com/nodejs/node-eps/pull/3#issuecomment-21476... . Basically we tried detection via source code as the first proposal; ambiguities at runtime that do not throw errors make it absolutely impossible to do safely, performance problems, and tooling integration problems.
Subjective, but .mjs just sounds horrid..
We looked at several alternative extensions and it was the least egregious of them: https://github.com/nodejs/node-eps/blob/master/002-es6-modul...
Why can't node parse a file to detect if it's a module? The presence of a top-level import or export means it's a module. If it's not, then the parsed file can be kept if the file is also in strict mode. If it's sloppy, it'll have to be re-parsed. Seems like a small penalty if the goal is to enable migration.
Also, why worry about ES modules importing Common JS? Just disallow that and let projects migrate to ES modules bottom-up. Then you don't have to worry about executing a Common JS module to determine what its exports are or circular dependency problems.